static void dump_confs(int step,t_atoms *atoms,
rvec x[],rvec xprime[],matrix box)
{
char buf[256];
sprintf(buf,"step%d.pdb",step-1);
write_sto_conf(buf,"one step before crash",atoms,x,NULL,box);
sprintf(buf,"step%d.pdb",step);
write_sto_conf(buf,"crashed",atoms,xprime,NULL,box);
if(stdlog)
fprintf(stdlog,"Wrote pdb files with previous and current coordinates\n");
fprintf(stderr,"Wrote pdb files with previous and current coordinates\n");
}
void visualize_images(const char *fn, int ePBC, matrix box)
{
t_atoms atoms;
rvec *img;
char *c, *ala;
int nat, i;
nat = NTRICIMG + 1;
init_t_atoms(&atoms, nat, FALSE);
atoms.nr = nat;
snew(img,nat);
/* FIXME: Constness should not be cast away */
c = (char *) "C";
ala = (char *) "ALA";
for (i = 0; i < nat; i++)
{
atoms.atomname[i] = &c;
atoms.atom[i].resind = i;
atoms.resinfo[i].name = &ala;
atoms.resinfo[i].nr = i + 1;
atoms.resinfo[i].chainid = 'A' + i / NCUCVERT;
}
calc_triclinic_images(box, img + 1);
write_sto_conf(fn, "Images", &atoms, img, NULL, ePBC, box);
free_t_atoms(&atoms, FALSE);
sfree(img);
}
void dump_conf(t_pull *pull,rvec x[],matrix box,t_topology *top,
int nout, real time)
{
char buf[128],buf2[128];
rvec tmp,tmp1,tmp2;
sprintf(buf,"out_%d.gro",nout);
nout++;
/* calculate the current positions of the center of mass of the grps
printed is pull - reference, so position with respect to reference
group
*/
if (pull->pull.n == 2) {
rvec_sub(pull->pull.x_unc[0],pull->ref.x_unc[0],tmp1);
rvec_sub(pull->pull.x_unc[1],pull->ref.x_unc[0],tmp2);
sprintf(buf2,"grp1:%8.3f%8.3f%8.3f grp2:%8.3f%8.3f%8.3f t:%8.3f",
tmp1[0],tmp1[1],tmp1[2],tmp2[0],tmp2[1],tmp2[2],time);
} else {
rvec_sub(pull->pull.x_unc[0],pull->ref.x_unc[0],tmp1);
sprintf(buf2,"grp1:%8.3f%8.3f%8.3f t:%8.3f",
tmp1[XX],tmp1[YY],tmp1[ZZ],time);
}
write_sto_conf(buf,buf2,&top->atoms,x,NULL,box);
}
void write_sto_conf_mtop(const char *outfile, const char *title,
gmx_mtop_t *mtop,
rvec x[], rvec *v, int ePBC, matrix box)
{
int ftp;
FILE *out;
t_atoms atoms;
ftp = fn2ftp(outfile);
switch (ftp)
{
case efGRO:
out = gmx_fio_fopen(outfile, "w");
write_hconf_mtop(out, title, mtop, 3, x, v, box);
gmx_fio_fclose(out);
break;
default:
/* This is a brute force approach which requires a lot of memory.
* We should implement mtop versions of all writing routines.
*/
atoms = gmx_mtop_global_atoms(mtop);
write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
done_atom(&atoms);
break;
}
}
void visualize_images(char *fn,int ePBC,matrix box)
{
t_atoms atoms;
rvec *img;
char *c,*ala;
int nat,i;
nat = NTRICIMG+1;
init_t_atoms(&atoms,nat,FALSE);
atoms.nr = nat;
snew(img,nat);
c = "C";
ala = "ALA";
for(i=0; i<nat; i++) {
atoms.atomname[i] = &c;
atoms.atom[i].resnr = i;
atoms.resname[i] = &ala;
atoms.atom[i].chain = 'A'+i/NCUCVERT;
}
calc_triclinic_images(box,img+1);
write_sto_conf(fn,"Images",&atoms,img,NULL,ePBC,box);
free_t_atoms(&atoms,FALSE);
sfree(img);
}
void write_bfactors(t_filenm *fnm, int nfile, atom_id *index, atom_id *a, int nslices, int ngrps, real **order, t_topology *top, real **distvals, output_env_t oenv)
{
/*function to write order parameters as B factors in PDB file using
first frame of trajectory*/
t_trxstatus *status;
int natoms;
t_trxframe fr, frout;
t_atoms useatoms;
int i, j, ctr, nout;
ngrps -= 2; /*we don't have an order parameter for the first or
last atom in each chain*/
nout = nslices*ngrps;
natoms = read_first_frame(oenv, &status, ftp2fn(efTRX, nfile, fnm), &fr,
TRX_NEED_X);
close_trj(status);
frout = fr;
frout.natoms = nout;
frout.bF = FALSE;
frout.bV = FALSE;
frout.x = 0;
snew(frout.x, nout);
init_t_atoms(&useatoms, nout, TRUE);
useatoms.nr = nout;
/*initialize PDBinfo*/
for (i = 0; i < useatoms.nr; ++i)
{
useatoms.pdbinfo[i].type = 0;
useatoms.pdbinfo[i].occup = 0.0;
useatoms.pdbinfo[i].bfac = 0.0;
useatoms.pdbinfo[i].bAnisotropic = FALSE;
}
for (j = 0, ctr = 0; j < nslices; j++)
{
for (i = 0; i < ngrps; i++, ctr++)
{
/*iterate along each chain*/
useatoms.pdbinfo[ctr].bfac = order[j][i+1];
if (distvals)
{
useatoms.pdbinfo[ctr].occup = distvals[j][i+1];
}
copy_rvec(fr.x[a[index[i+1]+j]], frout.x[ctr]);
useatoms.atomname[ctr] = top->atoms.atomname[a[index[i+1]+j]];
useatoms.atom[ctr] = top->atoms.atom[a[index[i+1]+j]];
useatoms.nres = max(useatoms.nres, useatoms.atom[ctr].resind+1);
useatoms.resinfo[useatoms.atom[ctr].resind] = top->atoms.resinfo[useatoms.atom[ctr].resind]; /*copy resinfo*/
}
}
write_sto_conf(opt2fn("-ob", nfile, fnm), "Order parameters", &useatoms, frout.x, NULL, frout.ePBC, frout.box);
sfree(frout.x);
free_t_atoms(&useatoms, FALSE);
}
void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
real qcut,gmx_bool bSave,real minarea,gmx_bool bPBC,
real dgs_default,gmx_bool bFindex, const output_env_t oenv)
{
FILE *fp,*fp2,*fp3=NULL,*vp;
const char *flegend[] = { "Hydrophobic", "Hydrophilic",
"Total", "D Gsolv" };
const char *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
const char *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
const char *vfile;
real t;
gmx_atomprop_t aps=NULL;
gmx_rmpbc_t gpbc=NULL;
t_trxstatus *status;
int ndefault;
int i,j,ii,nfr,natoms,flag,nsurfacedots,res;
rvec *xtop,*x;
matrix topbox,box;
t_topology top;
char title[STRLEN];
int ePBC;
gmx_bool bTop;
t_atoms *atoms;
gmx_bool *bOut,*bPhobic;
gmx_bool bConnelly;
gmx_bool bResAt,bITP,bDGsol;
real *radius,*dgs_factor=NULL,*area=NULL,*surfacedots=NULL;
real at_area,*atom_area=NULL,*atom_area2=NULL;
real *res_a=NULL,*res_area=NULL,*res_area2=NULL;
real totarea,totvolume,totmass=0,density,harea,tarea,fluc2;
atom_id **index,*findex;
int *nx,nphobic,npcheck,retval;
char **grpname,*fgrpname;
real dgsolv;
bITP = opt2bSet("-i",nfile,fnm);
bResAt = opt2bSet("-or",nfile,fnm) || opt2bSet("-oa",nfile,fnm) || bITP;
bTop = read_tps_conf(ftp2fn(efTPS,nfile,fnm),title,&top,&ePBC,
&xtop,NULL,topbox,FALSE);
atoms = &(top.atoms);
if (!bTop) {
fprintf(stderr,"No tpr file, will not compute Delta G of solvation\n");
bDGsol = FALSE;
} else {
bDGsol = strcmp(*(atoms->atomtype[0]),"?") != 0;
if (!bDGsol) {
fprintf(stderr,"Warning: your tpr file is too old, will not compute "
"Delta G of solvation\n");
} else {
printf("In case you use free energy of solvation predictions:\n");
please_cite(stdout,"Eisenberg86a");
}
}
aps = gmx_atomprop_init();
if ((natoms=read_first_x(oenv,&status,ftp2fn(efTRX,nfile,fnm),
&t,&x,box))==0)
gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
if ((ePBC != epbcXYZ) || (TRICLINIC(box))) {
fprintf(stderr,"\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
"Analysis based on vacuum simulations (with the possibility of evaporation)\n"
"will certainly crash the analysis.\n\n");
}
snew(nx,2);
snew(index,2);
snew(grpname,2);
fprintf(stderr,"Select a group for calculation of surface and a group for output:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),2,nx,index,grpname);
if (bFindex) {
fprintf(stderr,"Select a group of hydrophobic atoms:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),1,&nphobic,&findex,&fgrpname);
}
snew(bOut,natoms);
for(i=0; i<nx[1]; i++)
bOut[index[1][i]] = TRUE;
/* Now compute atomic readii including solvent probe size */
snew(radius,natoms);
snew(bPhobic,nx[0]);
if (bResAt) {
snew(atom_area,nx[0]);
snew(atom_area2,nx[0]);
snew(res_a,atoms->nres);
snew(res_area,atoms->nres);
snew(res_area2,atoms->nres);
}
if (bDGsol)
snew(dgs_factor,nx[0]);
/* Get a Van der Waals radius for each atom */
ndefault = 0;
for(i=0; (i<natoms); i++) {
if (!gmx_atomprop_query(aps,epropVDW,
*(atoms->resinfo[atoms->atom[i].resind].name),
*(atoms->atomname[i]),&radius[i]))
ndefault++;
/* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
radius[i] += solsize;
}
if (ndefault > 0)
fprintf(stderr,"WARNING: could not find a Van der Waals radius for %d atoms\n",ndefault);
/* Determine which atom is counted as hydrophobic */
if (bFindex) {
npcheck = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
for(j=0; (j<nphobic); j++) {
if (findex[j] == ii) {
bPhobic[i] = TRUE;
if (bOut[ii])
npcheck++;
}
}
}
if (npcheck != nphobic)
gmx_fatal(FARGS,"Consistency check failed: not all %d atoms in the hydrophobic index\n"
"found in the normal index selection (%d atoms)",nphobic,npcheck);
}
else
nphobic = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (!bFindex) {
bPhobic[i] = fabs(atoms->atom[ii].q) <= qcut;
if (bPhobic[i] && bOut[ii])
nphobic++;
}
if (bDGsol)
if (!gmx_atomprop_query(aps,epropDGsol,
*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomtype[ii]),&(dgs_factor[i])))
dgs_factor[i] = dgs_default;
if (debug)
fprintf(debug,"Atom %5d %5s-%5s: q= %6.3f, r= %6.3f, dgsol= %6.3f, hydrophobic= %s\n",
ii+1,*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomname[ii]),
atoms->atom[ii].q,radius[ii]-solsize,dgs_factor[i],
BOOL(bPhobic[i]));
}
fprintf(stderr,"%d out of %d atoms were classified as hydrophobic\n",
nphobic,nx[1]);
fp=xvgropen(opt2fn("-o",nfile,fnm),"Solvent Accessible Surface","Time (ps)",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp,asize(flegend) - (bDGsol ? 0 : 1),flegend,oenv);
vfile = opt2fn_null("-tv",nfile,fnm);
if (vfile) {
if (!bTop) {
gmx_fatal(FARGS,"Need a tpr file for option -tv");
}
vp=xvgropen(vfile,"Volume and Density","Time (ps)","",oenv);
xvgr_legend(vp,asize(vlegend),vlegend,oenv);
totmass = 0;
ndefault = 0;
for(i=0; (i<nx[0]); i++) {
real mm;
ii = index[0][i];
/*
if (!query_atomprop(atomprop,epropMass,
*(top->atoms.resname[top->atoms.atom[ii].resnr]),
*(top->atoms.atomname[ii]),&mm))
ndefault++;
totmass += mm;
*/
totmass += atoms->atom[ii].m;
}
if (ndefault)
fprintf(stderr,"WARNING: Using %d default masses for density calculation, which most likely are inaccurate\n",ndefault);
}
else
vp = NULL;
gmx_atomprop_destroy(aps);
if (bPBC)
gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
nfr=0;
do {
if (bPBC)
gmx_rmpbc(gpbc,natoms,box,x);
bConnelly = (nfr==0 && opt2bSet("-q",nfile,fnm));
if (bConnelly) {
if (!bTop)
gmx_fatal(FARGS,"Need a tpr file for Connelly plot");
flag = FLAG_ATOM_AREA | FLAG_DOTS;
} else {
flag = FLAG_ATOM_AREA;
}
if (vp) {
flag = flag | FLAG_VOLUME;
}
if (debug)
write_sto_conf("check.pdb","pbc check",atoms,x,NULL,ePBC,box);
retval = nsc_dclm_pbc(x,radius,nx[0],ndots,flag,&totarea,
&area,&totvolume,&surfacedots,&nsurfacedots,
index[0],ePBC,bPBC ? box : NULL);
if (retval)
gmx_fatal(FARGS,"Something wrong in nsc_dclm_pbc");
if (bConnelly)
connelly_plot(ftp2fn(efPDB,nfile,fnm),
nsurfacedots,surfacedots,x,atoms,
&(top.symtab),ePBC,box,bSave);
harea = 0;
tarea = 0;
dgsolv = 0;
if (bResAt)
for(i=0; i<atoms->nres; i++)
res_a[i] = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (bOut[ii]) {
at_area = area[i];
if (bResAt) {
atom_area[i] += at_area;
atom_area2[i] += sqr(at_area);
res_a[atoms->atom[ii].resind] += at_area;
}
tarea += at_area;
if (bDGsol)
dgsolv += at_area*dgs_factor[i];
if (bPhobic[i])
harea += at_area;
}
}
if (bResAt)
for(i=0; i<atoms->nres; i++) {
res_area[i] += res_a[i];
res_area2[i] += sqr(res_a[i]);
}
fprintf(fp,"%10g %10g %10g %10g",t,harea,tarea-harea,tarea);
if (bDGsol)
fprintf(fp," %10g\n",dgsolv);
else
fprintf(fp,"\n");
/* Print volume */
if (vp) {
density = totmass*AMU/(totvolume*NANO*NANO*NANO);
fprintf(vp,"%12.5e %12.5e %12.5e\n",t,totvolume,density);
}
if (area) {
sfree(area);
area = NULL;
}
if (surfacedots) {
sfree(surfacedots);
surfacedots = NULL;
}
nfr++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
if (bPBC)
gmx_rmpbc_done(gpbc);
fprintf(stderr,"\n");
close_trj(status);
ffclose(fp);
if (vp)
ffclose(vp);
/* if necessary, print areas per atom to file too: */
if (bResAt) {
for(i=0; i<atoms->nres; i++) {
res_area[i] /= nfr;
res_area2[i] /= nfr;
}
for(i=0; i<nx[0]; i++) {
atom_area[i] /= nfr;
atom_area2[i] /= nfr;
}
fprintf(stderr,"Printing out areas per atom\n");
fp = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue over the trajectory","Residue",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp, asize(or_and_oa_legend),or_and_oa_legend,oenv);
fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom over the trajectory","Atom #",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp2, asize(or_and_oa_legend),or_and_oa_legend,oenv);
if (bITP) {
fp3 = ftp2FILE(efITP,nfile,fnm,"w");
fprintf(fp3,"[ position_restraints ]\n"
"#define FCX 1000\n"
"#define FCY 1000\n"
"#define FCZ 1000\n"
"; Atom Type fx fy fz\n");
}
for(i=0; i<nx[0]; i++) {
ii = index[0][i];
res = atoms->atom[ii].resind;
if (i==nx[0]-1 || res!=atoms->atom[index[0][i+1]].resind) {
fluc2 = res_area2[res]-sqr(res_area[res]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp,"%10d %10g %10g\n",
atoms->resinfo[res].nr,res_area[res],sqrt(fluc2));
}
fluc2 = atom_area2[i]-sqr(atom_area[i]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp2,"%d %g %g\n",index[0][i]+1,atom_area[i],sqrt(fluc2));
if (bITP && (atom_area[i] > minarea))
fprintf(fp3,"%5d 1 FCX FCX FCZ\n",ii+1);
}
if (bITP)
ffclose(fp3);
ffclose(fp);
}
/* Be a good citizen, keep our memory free! */
sfree(x);
sfree(nx);
for(i=0;i<2;i++)
{
sfree(index[i]);
sfree(grpname[i]);
}
sfree(bOut);
sfree(radius);
sfree(bPhobic);
if(bResAt)
{
sfree(atom_area);
sfree(atom_area2);
sfree(res_a);
sfree(res_area);
sfree(res_area2);
}
if(bDGsol)
{
sfree(dgs_factor);
}
}
int gmx_helix(int argc,char *argv[])
{
const char *desc[] = {
"g_helix computes all kind of helix properties. First, the peptide",
"is checked to find the longest helical part. This is determined by",
"Hydrogen bonds and Phi/Psi angles.",
"That bit is fitted",
"to an ideal helix around the Z-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file radius.xvg). This is merely the",
"RMS deviation in two dimensions for all Calpha atoms.",
"it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file twist.xvg). The average helical angle per",
"residue is calculated. For alpha helix it is 100 degrees,",
"for 3-10 helices it will be smaller,",
"for 5-helices it will be larger.[BR]",
"[BB]3.[bb] Rise per residue (file rise.xvg). The helical rise per",
"residue is plotted as the difference in Z-coordinate between Ca",
"atoms. For an ideal helix this is 0.15 nm[BR]",
"[BB]4.[bb] Total helix length (file len-ahx.xvg). The total length",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"number of helical residues (see below).[BR]",
"[BB]5.[bb] Number of helical residues (file n-ahx.xvg). The title says",
"it all.[BR]",
"[BB]6.[bb] Helix Dipole, backbone only (file dip-ahx.xvg).[BR]",
"[BB]7.[bb] RMS deviation from ideal helix, calculated for the Calpha",
"atoms only (file rms-ahx.xvg).[BR]",
"[BB]8.[bb] Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).[BR]",
"[BB]9.[bb] Average Phi and Psi angles (file phipsi.xvg).[BR]",
"[BB]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]",
"[PAR]"
};
static const char *ppp[efhNR+2] = {
NULL, "RAD", "TWIST", "RISE", "LEN", "NHX", "DIP", "RMS", "CPHI",
"RMSA", "PHI", "PSI", "HB3", "HB4", "HB5", "CD222", NULL
};
static gmx_bool bCheck=FALSE,bFit=TRUE,bDBG=FALSE,bEV=FALSE;
static int rStart=0,rEnd=0,r0=1;
t_pargs pa [] = {
{ "-r0", FALSE, etINT, {&r0},
"The first residue number in the sequence" },
{ "-q", FALSE, etBOOL,{&bCheck},
"Check at every step which part of the sequence is helical" },
{ "-F", FALSE, etBOOL,{&bFit},
"Toggle fit to a perfect helix" },
{ "-db", FALSE, etBOOL,{&bDBG},
"Print debug info" },
{ "-prop", FALSE, etENUM, {ppp},
"Select property to weight eigenvectors with. WARNING experimental stuff" },
{ "-ev", FALSE, etBOOL,{&bEV},
"Write a new 'trajectory' file for ED" },
{ "-ahxstart", FALSE, etINT, {&rStart},
"First residue in helix" },
{ "-ahxend", FALSE, etINT, {&rEnd},
"Last residue in helix" }
};
typedef struct {
FILE *fp,*fp2;
gmx_bool bfp2;
const char *filenm;
const char *title;
const char *xaxis;
const char *yaxis;
real val;
} t_xvgrfile;
t_xvgrfile xf[efhNR] = {
{ NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)" , 0.0 },
{ NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 },
{ NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 },
{ NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 },
{ NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 },
{ NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "rmsa-ahx","Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
{ NULL, NULL,FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 },
{ NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL,FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz" , 0.0 },
{ NULL, NULL,FALSE, "helicity","Helicity per Residue", "Residue", "% of time" , 0.0 }
};
output_env_t oenv;
FILE *otrj;
char buf[54],prop[256];
t_trxstatus *status;
int natoms,nre,nres;
t_bb *bb;
int i,j,ai,m,nall,nbb,nca,teller,nSel=0;
atom_id *bbindex,*caindex,*allindex;
t_topology *top;
int ePBC;
rvec *x,*xref,*xav;
real t;
real rms,fac;
matrix box;
gmx_rmpbc_t gpbc=NULL;
gmx_bool bRange;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efG87, "-to", NULL, ffOPTWR },
{ efSTO, "-cz", "zconf",ffWRITE },
{ efSTO, "-co", "waver",ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
bRange=(opt2parg_bSet("-ahxstart",asize(pa),pa) &&
opt2parg_bSet("-ahxend",asize(pa),pa));
top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
natoms=read_first_x(oenv,&status,opt2fn("-f",NFILE,fnm),&t,&x,box);
if (opt2bSet("-to",NFILE,fnm)) {
otrj=opt2FILE("-to",NFILE,fnm,"w");
strcpy(prop,ppp[0]);
fprintf(otrj,"%s Weighted Trajectory: %d atoms, NO box\n",prop,natoms);
}
else
otrj=NULL;
if (natoms != top->atoms.nr)
gmx_fatal(FARGS,"Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
top->atoms.nr,natoms);
bb=mkbbind(ftp2fn(efNDX,NFILE,fnm),&nres,&nbb,r0,&nall,&allindex,
top->atoms.atomname,top->atoms.atom,top->atoms.resinfo);
snew(bbindex,natoms);
snew(caindex,nres);
fprintf(stderr,"nall=%d\n",nall);
/* Open output files, default x-axis is time */
for(i=0; (i<efhNR); i++) {
sprintf(buf,"%s.xvg",xf[i].filenm);
remove(buf);
xf[i].fp=xvgropen(buf,xf[i].title,
xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
xf[i].yaxis,oenv);
if (xf[i].bfp2) {
sprintf(buf,"%s.out",xf[i].filenm);
remove(buf);
xf[i].fp2=ffopen(buf,"w");
}
}
/* Read reference frame from tpx file to compute helix length */
snew(xref,top->atoms.nr);
read_tpx(ftp2fn(efTPX,NFILE,fnm),
NULL,NULL,&natoms,xref,NULL,NULL,NULL);
calc_hxprops(nres,bb,xref,box);
do_start_end(nres,bb,xref,&nbb,bbindex,&nca,caindex,bRange,rStart,rEnd);
sfree(xref);
if (bDBG) {
fprintf(stderr,"nca=%d, nbb=%d\n",nca,nbb);
pr_bb(stdout,nres,bb);
}
gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box);
snew(xav,natoms);
teller=0;
do {
if ((teller++ % 10) == 0)
fprintf(stderr,"\rt=%.2f",t);
gmx_rmpbc(gpbc,natoms,box,x);
calc_hxprops(nres,bb,x,box);
if (bCheck)
do_start_end(nres,bb,x,&nbb,bbindex,&nca,caindex,FALSE,0,0);
if (nca >= 5) {
rms=fit_ahx(nres,bb,natoms,nall,allindex,x,nca,caindex,box,bFit);
if (teller == 1) {
write_sto_conf(opt2fn("-cz",NFILE,fnm),"Helix fitted to Z-Axis",
&(top->atoms),x,NULL,ePBC,box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2,nca,caindex,x);
xf[efhTWIST].val = twist(xf[efhTWIST].fp2,nca,caindex,x);
xf[efhRISE].val = rise(nca,caindex,x);
xf[efhLEN].val = ahx_len(nca,caindex,x,box);
xf[efhCD222].val = ellipticity(nres,bb);
xf[efhDIP].val = dip(nbb,bbindex,x,top->atoms.atom);
xf[efhRMS].val = rms;
xf[efhCPHI].val = ca_phi(nca,caindex,x,box);
xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2,nres,bb);
for(j=0; (j<=efhCPHI); j++)
fprintf(xf[j].fp, "%10g %10g\n",t,xf[j].val);
av_phipsi(xf[efhPHI].fp,xf[efhPSI].fp,xf[efhPHI].fp2,xf[efhPSI].fp2,
t,nres,bb);
av_hblen(xf[efhHB3].fp,xf[efhHB3].fp2,
xf[efhHB4].fp,xf[efhHB4].fp2,
xf[efhHB5].fp,xf[efhHB5].fp2,
t,nres,bb);
if (otrj)
dump_otrj(otrj,nall,allindex,x,xf[nSel].val,xav);
}
} while (read_next_x(oenv,status,&t,natoms,x,box));
fprintf(stderr,"\n");
gmx_rmpbc_done(gpbc);
close_trj(status);
if (otrj) {
ffclose(otrj);
fac=1.0/teller;
for(i=0; (i<nall); i++) {
ai=allindex[i];
for(m=0; (m<DIM); m++)
xav[ai][m]*=fac;
}
write_sto_conf_indexed(opt2fn("-co",NFILE,fnm),
"Weighted and Averaged conformation",
&(top->atoms),xav,NULL,ePBC,box,nall,allindex);
}
for(i=0; (i<nres); i++) {
if (bb[i].nrms > 0) {
fprintf(xf[efhRMSA].fp,"%10d %10g\n",r0+i,bb[i].rmsa/bb[i].nrms);
}
fprintf(xf[efhAHX].fp,"%10d %10g\n",r0+i,(bb[i].nhx*100.0)/(real )teller);
fprintf(xf[efhJCA].fp,"%10d %10g\n",
r0+i,140.3+(bb[i].jcaha/(double)teller));
}
for(i=0; (i<efhNR); i++) {
ffclose(xf[i].fp);
if (xf[i].bfp2)
ffclose(xf[i].fp2);
do_view(oenv,xf[i].filenm,"-nxy");
}
thanx(stderr);
return 0;
}
int gmx_genion(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] randomly replaces solvent molecules with monoatomic ions.",
"The group of solvent molecules should be continuous and all molecules",
"should have the same number of atoms.",
"The user should add the ion molecules to the topology file or use",
"the [TT]-p[tt] option to automatically modify the topology.[PAR]",
"The ion molecule type, residue and atom names in all force fields",
"are the capitalized element names without sign. This molecule name",
"should be given with [TT]-pname[tt] or [TT]-nname[tt], and the",
"[TT][molecules][tt] section of your topology updated accordingly,",
"either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
"For larger ions, e.g. sulfate we recommended using [gmx-insert-molecules]."
};
const char *bugs[] = {
"If you specify a salt concentration existing ions are not taken into "
"account. In effect you therefore specify the amount of salt to be added.",
};
static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
static const char *p_name = "NA", *n_name = "CL";
static real rmin = 0.6, conc = 0;
static int seed = 1993;
static gmx_bool bNeutral = FALSE;
static t_pargs pa[] = {
{ "-np", FALSE, etINT, {&p_num}, "Number of positive ions" },
{ "-pname", FALSE, etSTR, {&p_name}, "Name of the positive ion" },
{ "-pq", FALSE, etINT, {&p_q}, "Charge of the positive ion" },
{ "-nn", FALSE, etINT, {&n_num}, "Number of negative ions" },
{ "-nname", FALSE, etSTR, {&n_name}, "Name of the negative ion" },
{ "-nq", FALSE, etINT, {&n_q}, "Charge of the negative ion" },
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance between ions" },
{ "-seed", FALSE, etINT, {&seed}, "Seed for random number generator" },
{ "-conc", FALSE, etREAL, {&conc},
"Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [REF].tpr[ref] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
{ "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
};
t_topology top;
rvec *x, *v;
real vol, qtot;
matrix box;
t_atoms atoms;
t_pbc pbc;
int *repl, ePBC;
atom_id *index;
char *grpname;
gmx_bool *bSet;
int i, nw, nwa, nsa, nsalt, iqtot;
gmx_output_env_t *oenv;
gmx_rng_t rng;
t_filenm fnm[] = {
{ efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTO, "-o", NULL, ffWRITE },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
/* Check input for something sensible */
if ((p_num < 0) || (n_num < 0))
{
gmx_fatal(FARGS, "Negative number of ions to add?");
}
if (conc > 0 && (p_num > 0 || n_num > 0))
{
fprintf(stderr, "WARNING: -conc specified, overriding -nn and -np.\n");
}
/* Read atom positions and charges */
read_tps_conf(ftp2fn(efTPR, NFILE, fnm), &top, &ePBC, &x, &v, box, FALSE);
atoms = top.atoms;
/* Compute total charge */
qtot = 0;
for (i = 0; (i < atoms.nr); i++)
{
qtot += atoms.atom[i].q;
}
iqtot = std::round(qtot);
if (conc > 0)
{
/* Compute number of ions to be added */
vol = det(box);
nsalt = std::round(conc*vol*AVOGADRO/1e24);
p_num = abs(nsalt*n_q);
n_num = abs(nsalt*p_q);
}
if (bNeutral)
{
int qdelta = p_num*p_q + n_num*n_q + iqtot;
/* Check if the system is neutralizable
* is (qdelta == p_q*p_num + n_q*n_num) solvable for p_num and n_num? */
int gcd = gmx_greatest_common_divisor(n_q, p_q);
if ((qdelta % gcd) != 0)
{
gmx_fatal(FARGS, "Can't neutralize this system using -nq %d and"
" -pq %d.\n", n_q, p_q);
}
while (qdelta != 0)
{
while (qdelta < 0)
{
p_num++;
qdelta += p_q;
}
while (qdelta > 0)
{
n_num++;
qdelta += n_q;
}
}
}
if ((p_num == 0) && (n_num == 0))
{
fprintf(stderr, "No ions to add, will just copy input configuration.\n");
}
else
{
printf("Will try to add %d %s ions and %d %s ions.\n",
p_num, p_name, n_num, n_name);
printf("Select a continuous group of solvent molecules\n");
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nwa, &index, &grpname);
for (i = 1; i < nwa; i++)
{
if (index[i] != index[i-1]+1)
{
gmx_fatal(FARGS, "The solvent group %s is not continuous: "
"index[%d]=%d, index[%d]=%d",
grpname, i, index[i-1]+1, i+1, index[i]+1);
}
}
nsa = 1;
while ((nsa < nwa) &&
(atoms.atom[index[nsa]].resind ==
atoms.atom[index[nsa-1]].resind))
{
nsa++;
}
if (nwa % nsa)
{
gmx_fatal(FARGS, "Your solvent group size (%d) is not a multiple of %d",
nwa, nsa);
}
nw = nwa/nsa;
fprintf(stderr, "Number of (%d-atomic) solvent molecules: %d\n", nsa, nw);
if (p_num+n_num > nw)
{
gmx_fatal(FARGS, "Not enough solvent for adding ions");
}
if (opt2bSet("-p", NFILE, fnm))
{
update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
}
snew(bSet, nw);
snew(repl, nw);
snew(v, atoms.nr);
snew(atoms.pdbinfo, atoms.nr);
set_pbc(&pbc, ePBC, box);
if (seed == 0)
{
rng = gmx_rng_init(gmx_rng_make_seed());
}
else
{
rng = gmx_rng_init(seed);
}
/* Now loop over the ions that have to be placed */
while (p_num-- > 0)
{
insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
1, p_q, p_name, &atoms, rmin, rng);
}
while (n_num-- > 0)
{
insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
-1, n_q, n_name, &atoms, rmin, rng);
}
gmx_rng_destroy(rng);
fprintf(stderr, "\n");
if (nw)
{
sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
}
sfree(atoms.pdbinfo);
atoms.pdbinfo = NULL;
}
write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC, box);
return 0;
}
static void project(const char *trajfile,t_topology *top,int ePBC,matrix topbox,
const char *projfile,const char *twodplotfile,
const char *threedplotfile, const char *filterfile,int skip,
const char *extremefile,gmx_bool bExtrAll,real extreme,
int nextr, t_atoms *atoms,int natoms,atom_id *index,
gmx_bool bFit,rvec *xref,int nfit,atom_id *ifit,real *w_rls,
real *sqrtm,rvec *xav,
int *eignr,rvec **eigvec,
int noutvec,int *outvec, gmx_bool bSplit,
const output_env_t oenv)
{
FILE *xvgrout=NULL;
int nat,i,j,d,v,vec,nfr,nframes=0,snew_size,frame;
t_trxstatus *out=NULL;
t_trxstatus *status;
int noutvec_extr,imin,imax;
real *pmin,*pmax;
atom_id *all_at;
matrix box;
rvec *xread,*x;
real t,inp,**inprod=NULL,min=0,max=0;
char str[STRLEN],str2[STRLEN],**ylabel,*c;
real fact;
gmx_rmpbc_t gpbc=NULL;
snew(x,natoms);
if (bExtrAll)
noutvec_extr=noutvec;
else
noutvec_extr=1;
if (trajfile) {
snew(inprod,noutvec+1);
if (filterfile) {
fprintf(stderr,"Writing a filtered trajectory to %s using eigenvectors\n",
filterfile);
for(i=0; i<noutvec; i++)
fprintf(stderr,"%d ",outvec[i]+1);
fprintf(stderr,"\n");
out=open_trx(filterfile,"w");
}
snew_size=0;
nfr=0;
nframes=0;
nat=read_first_x(oenv,&status,trajfile,&t,&xread,box);
if (nat>atoms->nr)
gmx_fatal(FARGS,"the number of atoms in your trajectory (%d) is larger than the number of atoms in your structure file (%d)",nat,atoms->nr);
snew(all_at,nat);
if (top)
gpbc = gmx_rmpbc_init(&top->idef,ePBC,nat,box);
for(i=0; i<nat; i++)
all_at[i]=i;
do {
if (nfr % skip == 0) {
if (top)
gmx_rmpbc(gpbc,nat,box,xread);
if (nframes>=snew_size) {
snew_size+=100;
for(i=0; i<noutvec+1; i++)
srenew(inprod[i],snew_size);
}
inprod[noutvec][nframes]=t;
/* calculate x: a fitted struture of the selected atoms */
if (bFit) {
reset_x(nfit,ifit,nat,NULL,xread,w_rls);
do_fit(nat,w_rls,xref,xread);
}
for (i=0; i<natoms; i++)
copy_rvec(xread[index[i]],x[i]);
for(v=0; v<noutvec; v++) {
vec=outvec[v];
/* calculate (mass-weighted) projection */
inp=0;
for (i=0; i<natoms; i++) {
inp+=(eigvec[vec][i][0]*(x[i][0]-xav[i][0])+
eigvec[vec][i][1]*(x[i][1]-xav[i][1])+
eigvec[vec][i][2]*(x[i][2]-xav[i][2]))*sqrtm[i];
}
inprod[v][nframes]=inp;
}
if (filterfile) {
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++) {
/* misuse xread for output */
xread[index[i]][d] = xav[i][d];
for(v=0; v<noutvec; v++)
xread[index[i]][d] +=
inprod[v][nframes]*eigvec[outvec[v]][i][d]/sqrtm[i];
}
write_trx(out,natoms,index,atoms,0,t,box,xread,NULL,NULL);
}
nframes++;
}
nfr++;
} while (read_next_x(oenv,status,&t,nat,xread,box));
close_trx(status);
sfree(x);
if (filterfile)
close_trx(out);
}
else
snew(xread,atoms->nr);
if (top)
gmx_rmpbc_done(gpbc);
if (projfile) {
snew(ylabel,noutvec);
for(v=0; v<noutvec; v++) {
sprintf(str,"vec %d",eignr[outvec[v]]+1);
ylabel[v]=strdup(str);
}
sprintf(str,"projection on eigenvectors (%s)",proj_unit);
write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
(const char **)ylabel,
nframes, inprod[noutvec], inprod, NULL,
output_env_get_time_factor(oenv), FALSE, bSplit,oenv);
}
if (twodplotfile) {
sprintf(str,"projection on eigenvector %d (%s)",
eignr[outvec[0]]+1,proj_unit);
sprintf(str2,"projection on eigenvector %d (%s)",
eignr[outvec[noutvec-1]]+1,proj_unit);
xvgrout=xvgropen(twodplotfile,"2D projection of trajectory",str,str2,
oenv);
for(i=0; i<nframes; i++) {
if ( bSplit && i>0 && abs(inprod[noutvec][i])<1e-5 )
fprintf(xvgrout,"&\n");
fprintf(xvgrout,"%10.5f %10.5f\n",inprod[0][i],inprod[noutvec-1][i]);
}
ffclose(xvgrout);
}
if (threedplotfile) {
t_atoms atoms;
rvec *x;
real *b=NULL;
matrix box;
char *resnm,*atnm, pdbform[STRLEN];
gmx_bool bPDB, b4D;
FILE *out;
if (noutvec < 3)
gmx_fatal(FARGS,"You have selected less than 3 eigenvectors");
/* initialize */
bPDB = fn2ftp(threedplotfile)==efPDB;
clear_mat(box);
box[XX][XX] = box[YY][YY] = box[ZZ][ZZ] = 1;
b4D = bPDB && (noutvec >= 4);
if (b4D) {
fprintf(stderr, "You have selected four or more eigenvectors:\n"
"fourth eigenvector will be plotted "
"in bfactor field of pdb file\n");
sprintf(str,"4D proj. of traj. on eigenv. %d, %d, %d and %d",
eignr[outvec[0]]+1,eignr[outvec[1]]+1,
eignr[outvec[2]]+1,eignr[outvec[3]]+1);
} else {
sprintf(str,"3D proj. of traj. on eigenv. %d, %d and %d",
eignr[outvec[0]]+1,eignr[outvec[1]]+1,eignr[outvec[2]]+1);
}
init_t_atoms(&atoms,nframes,FALSE);
snew(x,nframes);
snew(b,nframes);
atnm=strdup("C");
resnm=strdup("PRJ");
if(nframes>10000)
fact=10000.0/nframes;
else
fact=1.0;
for(i=0; i<nframes; i++) {
atoms.atomname[i] = &atnm;
atoms.atom[i].resind = i;
atoms.resinfo[i].name = &resnm;
atoms.resinfo[i].nr = ceil(i*fact);
atoms.resinfo[i].ic = ' ';
x[i][XX]=inprod[0][i];
x[i][YY]=inprod[1][i];
x[i][ZZ]=inprod[2][i];
if (b4D)
b[i] =inprod[3][i];
}
if ( ( b4D || bSplit ) && bPDB ) {
strcpy(pdbform,get_pdbformat());
strcat(pdbform,"%8.4f%8.4f\n");
out=ffopen(threedplotfile,"w");
fprintf(out,"HEADER %s\n",str);
if ( b4D )
fprintf(out,"REMARK %s\n","fourth dimension plotted as B-factor");
j=0;
for(i=0; i<atoms.nr; i++) {
if ( j>0 && bSplit && abs(inprod[noutvec][i])<1e-5 ) {
fprintf(out,"TER\n");
j=0;
}
fprintf(out,pdbform,"ATOM",i+1,"C","PRJ",' ',j+1,
PR_VEC(10*x[i]), 1.0, 10*b[i]);
if (j>0)
fprintf(out,"CONECT%5d%5d\n", i, i+1);
j++;
}
fprintf(out,"TER\n");
ffclose(out);
} else
write_sto_conf(threedplotfile,str,&atoms,x,NULL,ePBC,box);
free_t_atoms(&atoms,FALSE);
}
if (extremefile) {
snew(pmin,noutvec_extr);
snew(pmax,noutvec_extr);
if (extreme==0) {
fprintf(stderr,"%11s %17s %17s\n","eigenvector","Minimum","Maximum");
fprintf(stderr,
"%11s %10s %10s %10s %10s\n","","value","frame","value","frame");
imin = 0;
imax = 0;
for(v=0; v<noutvec_extr; v++) {
for(i=0; i<nframes; i++) {
if (inprod[v][i]<inprod[v][imin])
imin = i;
if (inprod[v][i]>inprod[v][imax])
imax = i;
}
pmin[v] = inprod[v][imin];
pmax[v] = inprod[v][imax];
fprintf(stderr,"%7d %10.6f %10d %10.6f %10d\n",
eignr[outvec[v]]+1,
pmin[v],imin,pmax[v],imax);
}
}
else {
pmin[0] = -extreme;
pmax[0] = extreme;
}
/* build format string for filename: */
strcpy(str,extremefile);/* copy filename */
c=strrchr(str,'.'); /* find where extention begins */
strcpy(str2,c); /* get extention */
sprintf(c,"%%d%s",str2); /* append '%s' and extention to filename */
for(v=0; v<noutvec_extr; v++) {
/* make filename using format string */
if (noutvec_extr==1)
strcpy(str2,extremefile);
else
sprintf(str2,str,eignr[outvec[v]]+1);
fprintf(stderr,"Writing %d frames along eigenvector %d to %s\n",
nextr,outvec[v]+1,str2);
out=open_trx(str2,"w");
for(frame=0; frame<nextr; frame++) {
if ((extreme==0) && (nextr<=3))
for(i=0; i<natoms; i++) {
atoms->resinfo[atoms->atom[index[i]].resind].chainid = 'A' + frame;
}
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++)
xread[index[i]][d] =
(xav[i][d] + (pmin[v]*(nextr-frame-1)+pmax[v]*frame)/(nextr-1)
*eigvec[outvec[v]][i][d]/sqrtm[i]);
write_trx(out,natoms,index,atoms,0,frame,topbox,xread,NULL,NULL);
}
close_trx(out);
}
sfree(pmin);
sfree(pmax);
}
fprintf(stderr,"\n");
}
int gmx_disre(int argc,char *argv[])
{
const char *desc[] = {
"g_disre computes violations of distance restraints.",
"If necessary all protons can be added to a protein molecule ",
"using the protonate program.[PAR]",
"The program always",
"computes the instantaneous violations rather than time-averaged,",
"because this analysis is done from a trajectory file afterwards",
"it does not make sense to use time averaging. However,",
"the time averaged values per restraint are given in the log file.[PAR]",
"An index file may be used to select specific restraints for",
"printing.[PAR]",
"When the optional[TT]-q[tt] flag is given a pdb file coloured by the",
"amount of average violations.[PAR]",
"When the [TT]-c[tt] option is given, an index file will be read",
"containing the frames in your trajectory corresponding to the clusters",
"(defined in another manner) that you want to analyze. For these clusters",
"the program will compute average violations using the third power",
"averaging algorithm and print them in the log file."
};
static int ntop = 0;
static int nlevels = 20;
static real max_dr = 0;
static gmx_bool bThird = TRUE;
t_pargs pa[] = {
{ "-ntop", FALSE, etINT, {&ntop},
"Number of large violations that are stored in the log file every step" },
{ "-maxdr", FALSE, etREAL, {&max_dr},
"Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data." },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels in the matrix output" },
{ "-third", FALSE, etBOOL, {&bThird},
"Use inverse third power averaging or linear for matrix output" }
};
FILE *out=NULL,*aver=NULL,*numv=NULL,*maxxv=NULL,*xvg=NULL;
t_tpxheader header;
t_inputrec ir;
gmx_mtop_t mtop;
rvec *xtop;
gmx_localtop_t *top;
t_atoms *atoms=NULL;
t_forcerec *fr;
t_fcdata fcd;
t_nrnb nrnb;
t_commrec *cr;
t_graph *g;
int ntopatoms,natoms,i,j,kkk;
t_trxstatus *status;
real t;
rvec *x,*f,*xav=NULL;
matrix box;
gmx_bool bPDB;
int isize;
atom_id *index=NULL,*ind_fit=NULL;
char *grpname;
t_cluster_ndx *clust=NULL;
t_dr_result dr,*dr_clust=NULL;
char **leg;
real *vvindex=NULL,*w_rls=NULL;
t_mdatoms *mdatoms;
t_pbc pbc,*pbc_null;
int my_clust;
FILE *fplog;
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-ds", "drsum", ffWRITE },
{ efXVG, "-da", "draver", ffWRITE },
{ efXVG, "-dn", "drnum", ffWRITE },
{ efXVG, "-dm", "drmax", ffWRITE },
{ efXVG, "-dr", "restr", ffWRITE },
{ efLOG, "-l", "disres", ffWRITE },
{ efNDX, NULL, "viol", ffOPTRD },
{ efPDB, "-q", "viol", ffOPTWR },
{ efNDX, "-c", "clust", ffOPTRD },
{ efXPM, "-x", "matrix", ffOPTWR }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,FALSE,0,&fplog);
if (ntop)
init5(ntop);
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&header,FALSE,NULL,NULL);
snew(xtop,header.natoms);
read_tpx(ftp2fn(efTPX,NFILE,fnm),&ir,box,&ntopatoms,xtop,NULL,NULL,&mtop);
bPDB = opt2bSet("-q",NFILE,fnm);
if (bPDB) {
snew(xav,ntopatoms);
snew(ind_fit,ntopatoms);
snew(w_rls,ntopatoms);
for(kkk=0; (kkk<ntopatoms); kkk++) {
w_rls[kkk] = 1;
ind_fit[kkk] = kkk;
}
snew(atoms,1);
*atoms = gmx_mtop_global_atoms(&mtop);
if (atoms->pdbinfo == NULL) {
snew(atoms->pdbinfo,atoms->nr);
}
}
top = gmx_mtop_generate_local_top(&mtop,&ir);
g = NULL;
pbc_null = NULL;
if (ir.ePBC != epbcNONE) {
if (ir.bPeriodicMols)
pbc_null = &pbc;
else
g = mk_graph(fplog,&top->idef,0,mtop.natoms,FALSE,FALSE);
}
if (ftp2bSet(efNDX,NFILE,fnm)) {
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
xvg=xvgropen(opt2fn("-dr",NFILE,fnm),"Inidividual Restraints","Time (ps)",
"nm",oenv);
snew(vvindex,isize);
snew(leg,isize);
for(i=0; (i<isize); i++) {
index[i]++;
snew(leg[i],12);
sprintf(leg[i],"index %d",index[i]);
}
xvgr_legend(xvg,isize,(const char**)leg,oenv);
}
else
isize=0;
ir.dr_tau=0.0;
init_disres(fplog,&mtop,&ir,NULL,FALSE,&fcd,NULL);
natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(f,5*natoms);
init_dr_res(&dr,fcd.disres.nres);
if (opt2bSet("-c",NFILE,fnm)) {
clust = cluster_index(fplog,opt2fn("-c",NFILE,fnm));
snew(dr_clust,clust->clust->nr+1);
for(i=0; (i<=clust->clust->nr); i++)
init_dr_res(&dr_clust[i],fcd.disres.nres);
}
else {
out =xvgropen(opt2fn("-ds",NFILE,fnm),
"Sum of Violations","Time (ps)","nm",oenv);
aver=xvgropen(opt2fn("-da",NFILE,fnm),
"Average Violation","Time (ps)","nm",oenv);
numv=xvgropen(opt2fn("-dn",NFILE,fnm),
"# Violations","Time (ps)","#",oenv);
maxxv=xvgropen(opt2fn("-dm",NFILE,fnm),
"Largest Violation","Time (ps)","nm",oenv);
}
mdatoms = init_mdatoms(fplog,&mtop,ir.efep!=efepNO);
atoms2md(&mtop,&ir,0,NULL,0,mtop.natoms,mdatoms);
update_mdatoms(mdatoms,ir.init_lambda);
fr = mk_forcerec();
fprintf(fplog,"Made forcerec\n");
init_forcerec(fplog,oenv,fr,NULL,&ir,&mtop,cr,box,FALSE,NULL,NULL,NULL,
FALSE,-1);
init_nrnb(&nrnb);
if (ir.ePBC != epbcNONE)
gpbc = gmx_rmpbc_init(&top->idef,ir.ePBC,natoms,box);
j=0;
do {
if (ir.ePBC != epbcNONE) {
if (ir.bPeriodicMols)
set_pbc(&pbc,ir.ePBC,box);
else
gmx_rmpbc(gpbc,natoms,box,x);
}
if (clust) {
if (j > clust->maxframe)
gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file. t = %8f\n",t);
my_clust = clust->inv_clust[j];
range_check(my_clust,0,clust->clust->nr);
check_viol(fplog,cr,&(top->idef.il[F_DISRES]),
top->idef.iparams,top->idef.functype,
x,f,fr,pbc_null,g,dr_clust,my_clust,isize,index,vvindex,&fcd);
}
else
check_viol(fplog,cr,&(top->idef.il[F_DISRES]),
top->idef.iparams,top->idef.functype,
x,f,fr,pbc_null,g,&dr,0,isize,index,vvindex,&fcd);
if (bPDB) {
reset_x(atoms->nr,ind_fit,atoms->nr,NULL,x,w_rls);
do_fit(atoms->nr,w_rls,x,x);
if (j == 0) {
/* Store the first frame of the trajectory as 'characteristic'
* for colouring with violations.
*/
for(kkk=0; (kkk<atoms->nr); kkk++)
copy_rvec(x[kkk],xav[kkk]);
}
}
if (!clust) {
if (isize > 0) {
fprintf(xvg,"%10g",t);
for(i=0; (i<isize); i++)
fprintf(xvg," %10g",vvindex[i]);
fprintf(xvg,"\n");
}
fprintf(out, "%10g %10g\n",t,dr.sumv);
fprintf(aver, "%10g %10g\n",t,dr.averv);
fprintf(maxxv,"%10g %10g\n",t,dr.maxv);
fprintf(numv, "%10g %10d\n",t,dr.nv);
}
j++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
close_trj(status);
if (ir.ePBC != epbcNONE)
gmx_rmpbc_done(gpbc);
if (clust) {
dump_clust_stats(fplog,fcd.disres.nres,&(top->idef.il[F_DISRES]),
top->idef.iparams,clust->clust,dr_clust,
clust->grpname,isize,index);
}
else {
dump_stats(fplog,j,fcd.disres.nres,&(top->idef.il[F_DISRES]),
top->idef.iparams,&dr,isize,index,
bPDB ? atoms : NULL);
if (bPDB) {
write_sto_conf(opt2fn("-q",NFILE,fnm),
"Coloured by average violation in Angstrom",
atoms,xav,NULL,ir.ePBC,box);
}
dump_disre_matrix(opt2fn_null("-x",NFILE,fnm),&dr,fcd.disres.nres,
j,&top->idef,&mtop,max_dr,nlevels,bThird);
ffclose(out);
ffclose(aver);
ffclose(numv);
ffclose(maxxv);
if (isize > 0) {
ffclose(xvg);
do_view(oenv,opt2fn("-dr",NFILE,fnm),"-nxy");
}
do_view(oenv,opt2fn("-dn",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-da",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-ds",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-dm",NFILE,fnm),"-nxy");
}
thanx(stderr);
if (gmx_parallel_env_initialized())
gmx_finalize();
gmx_log_close(fplog);
return 0;
}
int gmx_genconf(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] multiplies a given coordinate file by simply stacking them",
"on top of each other, like a small child playing with wooden blocks.",
"The program makes a grid of [IT]user-defined[it]",
"proportions ([TT]-nbox[tt]), ",
"and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
"When option [TT]-rot[tt] is used the program does not check for overlap",
"between molecules on grid points. It is recommended to make the box in",
"the input file at least as big as the coordinates + ",
"van der Waals radius.[PAR]",
"If the optional trajectory file is given, conformations are not",
"generated, but read from this file and translated appropriately to",
"build the grid."
};
const char *bugs[] = {
"The program should allow for random displacement of lattice points."
};
int vol;
t_atoms *atoms; /* list with all atoms */
rvec *x, *xx, *v; /* coordinates? */
real t;
vec4 *xrot, *vrot;
int ePBC;
matrix box, boxx; /* box length matrix */
rvec shift;
int natoms; /* number of atoms in one molecule */
int nres; /* number of molecules? */
int i, j, k, l, m, ndx, nrdx, nx, ny, nz;
t_trxstatus *status;
gmx_bool bTRX;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efSTO, "-o", "out", ffWRITE },
{ efTRX, "-trj", NULL, ffOPTRD }
};
#define NFILE asize(fnm)
static rvec nrbox = {1, 1, 1};
static int seed = 0; /* seed for random number generator */
static gmx_bool bRandom = FALSE; /* False: no random rotations */
static gmx_bool bRenum = TRUE; /* renumber residues */
static rvec dist = {0, 0, 0}; /* space added between molecules ? */
static rvec max_rot = {180, 180, 180}; /* maximum rotation */
t_pargs pa[] = {
{ "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
{ "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed (0 means generate)" },
{ "-rot", FALSE, etBOOL, {&bRandom}, "Randomly rotate conformations" },
{ "-maxrot", FALSE, etRVEC, {max_rot}, "Maximum random rotation" },
{ "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
if (seed == 0)
{
seed = static_cast<int>(gmx::makeRandomSeed());
}
gmx::DefaultRandomEngine rng(seed);
bTRX = ftp2bSet(efTRX, NFILE, fnm);
nx = (int)(nrbox[XX]+0.5);
ny = (int)(nrbox[YY]+0.5);
nz = (int)(nrbox[ZZ]+0.5);
if ((nx <= 0) || (ny <= 0) || (nz <= 0))
{
gmx_fatal(FARGS, "Number of boxes (-nbox) should be larger than zero");
}
vol = nx*ny*nz; /* calculate volume in grid points (= nr. molecules) */
t_topology *top;
snew(top, 1);
atoms = &top->atoms;
read_tps_conf(opt2fn("-f", NFILE, fnm), top, &ePBC, &x, &v, box, FALSE);
natoms = atoms->nr;
nres = atoms->nres; /* nr of residues in one element? */
/* make space for all the atoms */
add_t_atoms(atoms, natoms*(vol-1), nres*(vol-1));
srenew(x, natoms*vol); /* get space for coordinates of all atoms */
srenew(v, natoms*vol); /* velocities. not really needed? */
snew(xrot, natoms); /* get space for rotation matrix? */
snew(vrot, natoms);
if (bTRX)
{
if (!read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &xx, boxx))
{
gmx_fatal(FARGS, "No atoms in trajectory %s", ftp2fn(efTRX, NFILE, fnm));
}
}
else
{
snew(xx, natoms);
for (i = 0; i < natoms; i++)
{
copy_rvec(x[i], xx[i]);
}
}
for (k = 0; (k < nz); k++) /* loop over all gridpositions */
{
shift[ZZ] = k*(dist[ZZ]+box[ZZ][ZZ]);
for (j = 0; (j < ny); j++)
{
shift[YY] = j*(dist[YY]+box[YY][YY])+k*box[ZZ][YY];
for (i = 0; (i < nx); i++)
{
shift[XX] = i*(dist[XX]+box[XX][XX])+j*box[YY][XX]+k*box[ZZ][XX];
ndx = (i*ny*nz+j*nz+k)*natoms;
nrdx = (i*ny*nz+j*nz+k)*nres;
/* Random rotation on input coords */
if (bRandom)
{
rand_rot(natoms, xx, v, xrot, vrot, &rng, max_rot);
}
for (l = 0; (l < natoms); l++)
{
for (m = 0; (m < DIM); m++)
{
if (bRandom)
{
x[ndx+l][m] = xrot[l][m];
v[ndx+l][m] = vrot[l][m];
}
else
{
x[ndx+l][m] = xx[l][m];
v[ndx+l][m] = v[l][m];
}
}
if (ePBC == epbcSCREW && i % 2 == 1)
{
/* Rotate around x axis */
for (m = YY; m <= ZZ; m++)
{
x[ndx+l][m] = box[YY][m] + box[ZZ][m] - x[ndx+l][m];
v[ndx+l][m] = -v[ndx+l][m];
}
}
for (m = 0; (m < DIM); m++)
{
x[ndx+l][m] += shift[m];
}
atoms->atom[ndx+l].resind = nrdx + atoms->atom[l].resind;
atoms->atomname[ndx+l] = atoms->atomname[l];
}
for (l = 0; (l < nres); l++)
{
atoms->resinfo[nrdx+l] = atoms->resinfo[l];
if (bRenum)
{
atoms->resinfo[nrdx+l].nr += nrdx;
}
}
if (bTRX)
{
if (!read_next_x(oenv, status, &t, xx, boxx) &&
((i+1)*(j+1)*(k+1) < vol))
{
gmx_fatal(FARGS, "Not enough frames in trajectory");
}
}
}
}
}
if (bTRX)
{
close_trj(status);
}
/* make box bigger */
for (m = 0; (m < DIM); m++)
{
box[m][m] += dist[m];
}
svmul(nx, box[XX], box[XX]);
svmul(ny, box[YY], box[YY]);
svmul(nz, box[ZZ], box[ZZ]);
if (ePBC == epbcSCREW && nx % 2 == 0)
{
/* With an even number of boxes in x we can forgot about the screw */
ePBC = epbcXYZ;
}
/*depending on how you look at it, this is either a nasty hack or the way it should work*/
if (bRenum)
{
for (i = 0; i < atoms->nres; i++)
{
atoms->resinfo[i].nr = i+1;
}
}
write_sto_conf(opt2fn("-o", NFILE, fnm), *top->name, atoms, x, v, ePBC, box);
sfree(x);
sfree(v);
sfree(xrot);
sfree(vrot);
sfree(xx);
done_top(top);
sfree(top);
done_filenms(NFILE, fnm);
output_env_done(oenv);
return 0;
}
static bool HandleClient(t_x11 *x11, int ID, t_gmx *gmx)
{
t_pulldown *pd;
pd = gmx->pd;
switch (ID)
{
/* File Menu */
case IDDUMPWIN:
write_gmx(x11, gmx, IDDODUMP);
break;
case IDDODUMP:
if (gmx->man->bAnimate)
{
hide_but(x11, gmx->man->vbox);
}
dump_it(gmx->man);
if (gmx->man->bAnimate)
{
show_but(x11, gmx->man->vbox);
}
break;
case IDCLOSE:
case IDIMPORT:
case IDEXPORT:
ShowDlg(gmx->dlgs[edExport]);
break;
case IDDOEXPORT:
write_sto_conf(gmx->confout, *gmx->man->top.name,
&(gmx->man->top.atoms),
gmx->man->x, NULL, gmx->man->molw->ePBC, gmx->man->box);
break;
case IDQUIT:
show_mb(gmx, emQuit);
break;
case IDTERM:
done_gmx(x11, gmx);
return true;
/* Edit Menu */
case IDEDITTOP:
edit_file("topol.gmx");
break;
case IDEDITCOORDS:
edit_file("confin.gmx");
break;
case IDEDITPARAMS:
edit_file("mdparin.gmx");
break;
/* Display Menu */
case IDFILTER:
if (gmx->filter)
{
ShowDlg(gmx->dlgs[edFilter]);
}
break;
case IDDOFILTER:
do_filter(x11, gmx->man, gmx->filter);
break;
case IDANIMATE:
check_pd_item(pd, IDANIMATE, toggle_animate(x11, gmx->man));
break;
case IDLABELSOFF:
no_labels(x11, gmx->man);
break;
case IDRESETVIEW:
reset_view(gmx->man->view);
ExposeWin(x11->disp, gmx->man->molw->wd.self);
break;
case IDPHOTO:
show_mb(gmx, emNotImplemented);
break;
case IDBONDOPTS:
ShowDlg(gmx->dlgs[edBonds]);
break;
case IDTHIN:
set_bond_type(x11, gmx->man->molw, eBThin);
break;
case IDFAT:
set_bond_type(x11, gmx->man->molw, eBFat);
break;
case IDVERYFAT:
set_bond_type(x11, gmx->man->molw, eBVeryFat);
break;
case IDBALLS:
set_bond_type(x11, gmx->man->molw, eBSpheres);
break;
case IDNOBOX:
set_box_type(x11, gmx->man->molw, esbNone);
break;
case IDRECTBOX:
set_box_type(x11, gmx->man->molw, esbRect);
break;
case IDTRIBOX:
set_box_type(x11, gmx->man->molw, esbTri);
break;
case IDTOBOX:
set_box_type(x11, gmx->man->molw, esbTrunc);
break;
/* Analysis Menu */
case IDBOND:
case IDANGLE:
case IDDIH:
case IDRMS:
case IDRDF:
case IDENERGIES:
case IDCORR:
show_mb(gmx, emNotImplemented);
break;
/* Help Menu */
case IDHELP:
show_mb(gmx, emHelp);
break;
case IDABOUT:
show_logo(x11, gmx->logo);
break;
default:
break;
}
return false;
}
int gmx_insert_molecules(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] inserts [TT]-nmol[tt] copies of the system specified in",
"the [TT]-ci[tt] input file. The insertions take place either into",
"vacant space in the solute conformation given with [TT]-f[tt], or",
"into an empty box given by [TT]-box[tt]. Specifying both [TT]-f[tt]",
"and [TT]-box[tt] behaves like [TT]-f[tt], but places a new box",
"around the solute before insertions. Any velocities present are",
"discarded.[PAR]",
"By default, the insertion positions are random (with initial seed",
"specified by [TT]-seed[tt]). The program iterates until [TT]-nmol[tt]",
"molecules have been inserted in the box. Molecules are not inserted",
"where the distance between any existing atom and any atom of the",
"inserted molecule is less than the sum based on the van der Waals",
"radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
"Waals radii is read by the program, and the resulting radii scaled",
"by [TT]-scale[tt]. If radii are not found in the database, those"
"atoms are assigned the (pre-scaled) distance [TT]-radius[tt].[PAR]",
"A total of [TT]-nmol[tt] * [TT]-try[tt] insertion attempts are made",
"before giving up. Increase [TT]-try[tt] if you have several small",
"holes to fill. Option [TT]-rot[tt] specifies whether the insertion",
"molecules are randomly oriented before insertion attempts.[PAR]",
"Alternatively, the molecules can be inserted only at positions defined in",
"positions.dat ([TT]-ip[tt]). That file should have 3 columns (x,y,z),",
"that give the displacements compared to the input molecule position",
"([TT]-ci[tt]). Hence, if that file should contain the absolute",
"positions, the molecule must be centered on (0,0,0) before using",
"[THISMODULE] (e.g. from [gmx-editconf] [TT]-center[tt]).",
"Comments in that file starting with # are ignored. Option [TT]-dr[tt]",
"defines the maximally allowed displacements during insertial trials.",
"[TT]-try[tt] and [TT]-rot[tt] work as in the default mode (see above).",
"[PAR]",
};
/* parameter data */
real *exclusionDistances = NULL;
real *exclusionDistances_insrt = NULL;
/* protein configuration data */
char *title = NULL;
t_atoms *atoms, *atoms_insrt;
rvec *x = NULL, *x_insrt = NULL;
int ePBC = -1;
matrix box;
t_filenm fnm[] = {
{ efSTX, "-f", "protein", ffOPTRD },
{ efSTX, "-ci", "insert", ffREAD},
{ efDAT, "-ip", "positions", ffOPTRD},
{ efSTO, NULL, NULL, ffWRITE},
};
#define NFILE asize(fnm)
static int nmol_ins = 0, nmol_try = 10, seed = 1997;
static real defaultDistance = 0.105, scaleFactor = 0.57;
static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
output_env_t oenv;
const char *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
"Box size (in nm)" },
{ "-nmol", FALSE, etINT, {&nmol_ins},
"Number of extra molecules to insert" },
{ "-try", FALSE, etINT, {&nmol_try},
"Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed"},
{ "-radius", FALSE, etREAL, {&defaultDistance},
"Default van der Waals distance"},
{ "-scale", FALSE, etREAL, {&scaleFactor},
"Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
{ "-dr", FALSE, etRVEC, {deltaR},
"Allowed displacement in x/y/z from positions in [TT]-ip[tt] file" },
{ "-rot", FALSE, etENUM, {enum_rot_string},
"rotate inserted molecules randomly" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
const bool bProt = opt2bSet("-f", NFILE, fnm);
const bool bBox = opt2parg_bSet("-box", asize(pa), pa);
const char *const posfn = opt2fn_null("-ip", NFILE, fnm);
const int enum_rot = nenum(enum_rot_string);
/* check input */
if (nmol_ins <= 0 && !opt2bSet("-ip", NFILE, fnm))
{
gmx_fatal(FARGS, "Either -nmol must be larger than 0, "
"or positions must be given with -ip");
}
if (!bProt && !bBox)
{
gmx_fatal(FARGS, "When no solute (-f) is specified, "
"a box size (-box) must be specified");
}
gmx_atomprop_t aps = gmx_atomprop_init();
snew(atoms, 1);
init_t_atoms(atoms, 0, FALSE);
if (bProt)
{
/* Generate a solute configuration */
const char *conf_prot = opt2fn("-f", NFILE, fnm);
title = readConformation(conf_prot, atoms, &x, NULL,
&ePBC, box);
exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
if (atoms->nr == 0)
{
fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
sfree(title);
title = NULL;
}
}
if (bBox)
{
ePBC = epbcXYZ;
clear_mat(box);
box[XX][XX] = new_box[XX];
box[YY][YY] = new_box[YY];
box[ZZ][ZZ] = new_box[ZZ];
}
if (det(box) == 0)
{
gmx_fatal(FARGS, "Undefined solute box.\nCreate one with gmx editconf "
"or give explicit -box command line option");
}
snew(atoms_insrt, 1);
init_t_atoms(atoms_insrt, 0, FALSE);
{
int ePBC_dummy;
matrix box_dummy;
const char *conf_insrt = opt2fn("-ci", NFILE, fnm);
char *title_ins
= readConformation(conf_insrt, atoms_insrt, &x_insrt, NULL,
&ePBC_dummy, box_dummy);
if (atoms_insrt->nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input", conf_insrt);
}
if (title == NULL)
{
title = title_ins;
}
else
{
sfree(title_ins);
}
if (posfn == NULL)
{
center_molecule(atoms_insrt->nr, x_insrt);
}
exclusionDistances_insrt = makeExclusionDistances(atoms_insrt, aps, defaultDistance, scaleFactor);
}
gmx_atomprop_destroy(aps);
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
insert_mols(nmol_ins, nmol_try, seed,
atoms, &x, &exclusionDistances,
atoms_insrt, x_insrt, exclusionDistances_insrt,
ePBC, box, posfn, deltaR, enum_rot);
/* write new configuration to file confout */
const char *confout = ftp2fn(efSTO, NFILE, fnm);
fprintf(stderr, "Writing generated configuration to %s\n", confout);
write_sto_conf(confout, title, atoms, x, NULL, ePBC, box);
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
atoms->nr, atoms->nres);
sfree(exclusionDistances);
sfree(exclusionDistances_insrt);
sfree(x);
done_atom(atoms);
done_atom(atoms_insrt);
sfree(atoms);
sfree(atoms_insrt);
sfree(title);
return 0;
}
int gmx_confrms(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_confrms[tt] computes the root mean square deviation (RMSD) of two",
"structures after least-squares fitting the second structure on the first one.",
"The two structures do NOT need to have the same number of atoms,",
"only the two index groups used for the fit need to be identical.",
"With [TT]-name[tt] only matching atom names from the selected groups",
"will be used for the fit and RMSD calculation. This can be useful ",
"when comparing mutants of a protein.",
"[PAR]",
"The superimposed structures are written to file. In a [TT].pdb[tt] file",
"the two structures will be written as separate models",
"(use [TT]rasmol -nmrpdb[tt]). Also in a [TT].pdb[tt] file, B-factors",
"calculated from the atomic MSD values can be written with [TT]-bfac[tt].",
};
static gmx_bool bOne = FALSE, bRmpbc = FALSE, bMW = TRUE, bName = FALSE,
bBfac = FALSE, bFit = TRUE, bLabel = FALSE;
t_pargs pa[] = {
{ "-one", FALSE, etBOOL, {&bOne}, "Only write the fitted structure to file" },
{ "-mw", FALSE, etBOOL, {&bMW}, "Mass-weighted fitting and RMSD" },
{ "-pbc", FALSE, etBOOL, {&bRmpbc}, "Try to make molecules whole again" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Do least squares superposition of the target structure to the reference" },
{ "-name", FALSE, etBOOL, {&bName},
"Only compare matching atom names" },
{ "-label", FALSE, etBOOL, {&bLabel},
"Added chain labels A for first and B for second structure"},
{ "-bfac", FALSE, etBOOL, {&bBfac},
"Output B-factors from atomic MSD values" }
};
t_filenm fnm[] = {
{ efTPS, "-f1", "conf1.gro", ffREAD },
{ efSTX, "-f2", "conf2", ffREAD },
{ efSTO, "-o", "fit.pdb", ffWRITE },
{ efNDX, "-n1", "fit1.ndx", ffOPTRD },
{ efNDX, "-n2", "fit2.ndx", ffOPTRD },
{ efNDX, "-no", "match.ndx", ffOPTWR }
};
#define NFILE asize(fnm)
/* the two structure files */
const char *conf1file, *conf2file, *matchndxfile, *outfile;
FILE *fp;
char title1[STRLEN], title2[STRLEN], *name1, *name2;
t_topology *top1, *top2;
int ePBC1, ePBC2;
t_atoms *atoms1, *atoms2;
int warn = 0;
atom_id at;
real *w_rls, mass, totmass;
rvec *x1, *v1, *x2, *v2, *fit_x;
matrix box1, box2;
output_env_t oenv;
/* counters */
int i, j, m;
/* center of mass calculation */
real tmas1, tmas2;
rvec xcm1, xcm2;
/* variables for fit */
char *groupnames1, *groupnames2;
int isize1, isize2;
atom_id *index1, *index2;
real rms, msd, minmsd, maxmsd;
real *msds;
parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
matchndxfile = opt2fn_null("-no", NFILE, fnm);
conf1file = ftp2fn(efTPS, NFILE, fnm);
conf2file = ftp2fn(efSTX, NFILE, fnm);
/* reading reference structure from first structure file */
fprintf(stderr, "\nReading first structure file\n");
snew(top1, 1);
read_tps_conf(conf1file, title1, top1, &ePBC1, &x1, &v1, box1, TRUE);
atoms1 = &(top1->atoms);
fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
title1, atoms1->nr, atoms1->nres);
if (bRmpbc)
{
rm_gropbc(atoms1, x1, box1);
}
fprintf(stderr, "Select group from first structure\n");
get_index(atoms1, opt2fn_null("-n1", NFILE, fnm),
1, &isize1, &index1, &groupnames1);
printf("\n");
if (bFit && (isize1 < 3))
{
gmx_fatal(FARGS, "Need >= 3 points to fit!\n");
}
/* reading second structure file */
fprintf(stderr, "\nReading second structure file\n");
snew(top2, 1);
read_tps_conf(conf2file, title2, top2, &ePBC2, &x2, &v2, box2, TRUE);
atoms2 = &(top2->atoms);
fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
title2, atoms2->nr, atoms2->nres);
if (bRmpbc)
{
rm_gropbc(atoms2, x2, box2);
}
fprintf(stderr, "Select group from second structure\n");
get_index(atoms2, opt2fn_null("-n2", NFILE, fnm),
1, &isize2, &index2, &groupnames2);
if (bName)
{
find_matching_names(&isize1, index1, atoms1, &isize2, index2, atoms2);
if (matchndxfile)
{
fp = ffopen(matchndxfile, "w");
fprintf(fp, "; Matching atoms between %s from %s and %s from %s\n",
groupnames1, conf1file, groupnames2, conf2file);
fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
for (i = 0; i < isize1; i++)
{
fprintf(fp, "%4u%s", index1[i]+1, (i%15 == 14 || i == isize1-1) ? "\n" : " ");
}
fprintf(fp, "[ Match_%s_%s ]\n", conf2file, groupnames2);
for (i = 0; i < isize2; i++)
{
fprintf(fp, "%4u%s", index2[i]+1, (i%15 == 14 || i == isize2-1) ? "\n" : " ");
}
}
}
/* check isizes, must be equal */
if (isize2 != isize1)
{
gmx_fatal(FARGS, "You selected groups with differen number of atoms.\n");
}
for (i = 0; i < isize1; i++)
{
name1 = *atoms1->atomname[index1[i]];
name2 = *atoms2->atomname[index2[i]];
if (strcmp(name1, name2))
{
if (warn < 20)
{
fprintf(stderr,
"Warning: atomnames at index %d don't match: %u %s, %u %s\n",
i+1, index1[i]+1, name1, index2[i]+1, name2);
}
warn++;
}
if (!bMW)
{
atoms1->atom[index1[i]].m = 1;
atoms2->atom[index2[i]].m = 1;
}
}
if (warn)
{
fprintf(stderr, "%d atomname%s did not match\n", warn, (warn == 1) ? "" : "s");
}
if (bFit)
{
/* calculate and remove center of mass of structures */
calc_rm_cm(isize1, index1, atoms1, x1, xcm1);
calc_rm_cm(isize2, index2, atoms2, x2, xcm2);
snew(w_rls, atoms2->nr);
snew(fit_x, atoms2->nr);
for (at = 0; (at < isize1); at++)
{
w_rls[index2[at]] = atoms1->atom[index1[at]].m;
copy_rvec(x1[index1[at]], fit_x[index2[at]]);
}
/* do the least squares fit to the reference structure */
do_fit(atoms2->nr, w_rls, fit_x, x2);
sfree(fit_x);
sfree(w_rls);
w_rls = NULL;
}
else
{
clear_rvec(xcm1);
clear_rvec(xcm2);
w_rls = NULL;
}
/* calculate the rms deviation */
rms = 0;
totmass = 0;
maxmsd = -1e18;
minmsd = 1e18;
snew(msds, isize1);
for (at = 0; at < isize1; at++)
{
mass = atoms1->atom[index1[at]].m;
for (m = 0; m < DIM; m++)
{
msd = sqr(x1[index1[at]][m] - x2[index2[at]][m]);
rms += msd*mass;
msds[at] += msd;
}
maxmsd = max(maxmsd, msds[at]);
minmsd = min(minmsd, msds[at]);
totmass += mass;
}
rms = sqrt(rms/totmass);
printf("Root mean square deviation after lsq fit = %g nm\n", rms);
if (bBfac)
{
printf("Atomic MSD's range from %g to %g nm^2\n", minmsd, maxmsd);
}
if (bFit)
{
/* reset coordinates of reference and fitted structure */
for (i = 0; i < atoms1->nr; i++)
{
for (m = 0; m < DIM; m++)
{
x1[i][m] += xcm1[m];
}
}
for (i = 0; i < atoms2->nr; i++)
{
for (m = 0; m < DIM; m++)
{
x2[i][m] += xcm1[m];
}
}
}
outfile = ftp2fn(efSTO, NFILE, fnm);
switch (fn2ftp(outfile))
{
case efPDB:
case efBRK:
case efENT:
if (bBfac || bLabel)
{
srenew(atoms1->pdbinfo, atoms1->nr);
srenew(atoms1->atom, atoms1->nr); /* Why renew atom? */
/* Avoid segfaults when writing the pdb-file */
for (i = 0; i < atoms1->nr; i++)
{
atoms1->pdbinfo[i].type = eptAtom;
atoms1->pdbinfo[i].occup = 1.00;
atoms1->pdbinfo[i].bAnisotropic = FALSE;
if (bBfac)
{
atoms1->pdbinfo[i].bfac = 0;
}
if (bLabel)
{
atoms1->resinfo[atoms1->atom[i].resind].chainid = 'A';
}
}
for (i = 0; i < isize1; i++)
{
/* atoms1->pdbinfo[index1[i]].type = eptAtom; */
/* atoms1->pdbinfo[index1[i]].bAnisotropic = FALSE; */
if (bBfac)
{
atoms1->pdbinfo[index1[i]].bfac = (800*M_PI*M_PI/3.0)*msds[i];
}
/* if (bLabel) */
/* atoms1->resinfo[atoms1->atom[index1[i]].resind].chain = 'A'; */
}
srenew(atoms2->pdbinfo, atoms2->nr);
srenew(atoms2->atom, atoms2->nr); /* Why renew atom? */
for (i = 0; i < atoms2->nr; i++)
{
atoms2->pdbinfo[i].type = eptAtom;
atoms2->pdbinfo[i].occup = 1.00;
atoms2->pdbinfo[i].bAnisotropic = FALSE;
if (bBfac)
{
atoms2->pdbinfo[i].bfac = 0;
}
if (bLabel)
{
atoms2->resinfo[atoms1->atom[i].resind].chainid = 'B';
}
}
for (i = 0; i < isize2; i++)
{
/* atoms2->pdbinfo[index2[i]].type = eptAtom; */
/* atoms2->pdbinfo[index2[i]].bAnisotropic = FALSE; */
if (bBfac)
{
atoms2->pdbinfo[index2[i]].bfac = (800*M_PI*M_PI/3.0)*msds[i];
}
/* if (bLabel) */
/* atoms2->resinfo[atoms2->atom[index2[i]].resind].chain = 'B'; */
}
}
fp = ffopen(outfile, "w");
if (!bOne)
{
write_pdbfile(fp, title1, atoms1, x1, ePBC1, box1, ' ', 1, NULL, TRUE);
}
write_pdbfile(fp, title2, atoms2, x2, ePBC2, box2, ' ', bOne ? -1 : 2, NULL, TRUE);
ffclose(fp);
break;
case efGRO:
if (bBfac)
{
fprintf(stderr, "WARNING: cannot write B-factor values to gro file\n");
}
fp = ffopen(outfile, "w");
if (!bOne)
{
write_hconf_p(fp, title1, atoms1, 3, x1, v1, box1);
}
write_hconf_p(fp, title2, atoms2, 3, x2, v2, box2);
ffclose(fp);
break;
default:
if (bBfac)
{
fprintf(stderr, "WARNING: cannot write B-factor values to %s file\n",
ftp2ext(fn2ftp(outfile)));
}
if (!bOne)
{
fprintf(stderr,
"WARNING: cannot write the reference structure to %s file\n",
ftp2ext(fn2ftp(outfile)));
}
write_sto_conf(outfile, title2, atoms2, x2, v2, ePBC2, box2);
break;
}
view_all(oenv, NFILE, fnm);
thanx(stderr);
return 0;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"[TT]mkice[tt] generates an ice crystal in the Ih crystal form which is the",
"most stable form. The rectangular unitcell contains eight molecules",
"and all oxygens are tetrahedrally coordinated.[PAR]",
"If an input file is given it is interpreted as a series of oxygen",
"coordinates the distance between which can be scaled by the odist flag.",
"The program then adds hydrogens to the oxygens in random orientation",
"but with proper OH distances and HOH angle. This feature allows to",
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
static gmx_bool bYaw=FALSE,bLJ=TRUE,bFull=TRUE,bSeries=FALSE;
static gmx_bool bOrdered=TRUE,bDiamond=FALSE,bPBC=TRUE;
static real rcut=0.3,odist=0.274,hdist=0.09572;
t_pargs pa[] = {
{ "-nx", FALSE, etINT, {&nx}, "nx" },
{ "-ny", FALSE, etINT, {&ny}, "ny" },
{ "-nz", FALSE, etINT, {&nz}, "nz" },
{ "-yaw", FALSE, etBOOL, {&bYaw},
"Generate virtual sites and shell positions" },
{ "-lj", FALSE, etBOOL, {&bLJ},
"Use LJ as well as coulomb for virial calculation" },
{ "-rcut", FALSE,etREAL, {&rcut},"Cut-off for virial calculations" },
{ "-full", FALSE,etBOOL, {&bFull},"Full virial output" },
{ "-odist", FALSE, etREAL, {&odist}, "Distance (nm) between oxygens" },
{ "-hdist", FALSE, etREAL, {&hdist}, "Bondlength (nm) for OH bond" },
{ "-diamond",FALSE,etBOOL, {&bDiamond}, "Make a diamond instead" },
{ "-pbc", FALSE, etBOOL, {&bPBC}, "Make a periodic diamond" },
{ "-order", FALSE,etBOOL, {&bOrdered}, "Make a proton-ordered ice lattice" },
{ "-series",FALSE, etBOOL, {&bSeries},
"Do a series of virial calculations with different cut-off (from 0.3 up till the specified one)" }
};
t_filenm fnm[] = {
{ efSTO, "-p", "ice", ffWRITE },
{ efSTO, "-c", NULL, ffOPTRD },
{ efDAT, "-f", NULL, ffOPTRD },
{ efTRN, "-o", "ice", ffOPTWR }
};
#define NFILE asize(fnm)
FILE *fp;
char *fn,quote[256];
int i,j,k,n,nmax,m,natom,natmol;
t_atoms *pdba;
t_atoms atoms;
t_symtab symtab;
rvec box,tmp,*xx;
matrix boxje;
CopyRight(stdout,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,asize(desc),
desc,0,NULL);
if (debug) {
fprintf(debug,"nx = %3d, ny = %3d, nz = %3d\n",nx,ny,nz);
fprintf(debug,"YAW = %3s, LJ = %3s, rcut = %g\n",yesno_names[bYaw],
yesno_names[bLJ],rcut);
}
if (bYaw)
natmol = 5;
else if (bDiamond)
natmol = 1;
else
natmol = 3;
if (opt2bSet("-f",NFILE,fnm)) {
natom = read_rel_coords(opt2fn("-f",NFILE,fnm),&xx,natmol);
nmax = natom;
}
else {
natom = natmol*8;
nmax = natom*nx*ny*nz;
snew(xx,nmax);
}
snew(pdba,1);
init_t_atoms(pdba,nmax,TRUE);
pdba->nr = nmax;
open_symtab(&symtab);
for(n=0; (n<nmax); n++) {
pdba->pdbinfo[n].type = epdbATOM;
pdba->pdbinfo[n].atomnr = 1+n;
pdba->atom[n].resnr = 1+(n/natmol);
pdba->atomname[n] = put_symtab(&symtab,
bDiamond ? diamname[(n % natmol)] : watname[(n % natmol)]);
if (bDiamond)
pdba->resname[n] = put_symtab(&symtab,"DIA");
else
pdba->resname[n] = put_symtab(&symtab,"SOL");
sprintf(pdba->pdbinfo[n].pdbresnr,"%d",n);
pdba->atom[n].chain = ' ';
}
/* Generate the unit cell */
if (bDiamond)
unitcell_d(xx,box,odist);
else if (opt2bSet("-f",NFILE,fnm)) {
random_h_coords(natmol,natom/natmol,xx,box,bYaw,odist,hdist);
}
else
unitcell(xx,box,bYaw,odist,hdist);
if (debug) {
clear_mat(boxje);
boxje[XX][XX] = box[XX];
boxje[YY][YY] = box[YY];
boxje[ZZ][ZZ] = box[ZZ];
}
n=0;
for(i=0; (i<nx); i++) {
tmp[XX] = i*box[XX];
for(j=0; (j<ny); j++) {
tmp[YY] = j*box[YY];
for(k=0; (k<nz); k++) {
tmp[ZZ] = k*box[ZZ];
for(m=0; (m<natom); m++,n++) {
if ((!bOrdered && ((m % natmol) == 0)) || bOrdered)
rvec_add(xx[n % natom],tmp,xx[n]);
else
;
}
}
}
}
clear_mat(boxje);
boxje[XX][XX] = box[XX]*nx;
boxje[YY][YY] = box[YY]*ny;
boxje[ZZ][ZZ] = box[ZZ]*nz;
printf("Crystal: %10.5f %10.5f %10.5f\n",
nx*box[XX],ny*box[YY],nz*box[ZZ]);
if (debug && !bDiamond) {
if (bSeries)
for(i=3; (i<=10*rcut); i++) {
fprintf(debug,"This is with rcut = %g\n",i*0.1);
virial(debug,bFull,nmax/natmol,xx,boxje,
0.1*i,bYaw,bYaw ? qyaw : qspc,bLJ);
}
else
virial(debug,bFull,nmax/natmol,xx,boxje,
rcut,bYaw,bYaw ? qyaw : qspc,bLJ);
}
if (bDiamond)
mk_diamond(pdba,xx,odist,&symtab,bPBC,boxje);
fn = ftp2fn(efSTO,NFILE,fnm);
if (fn2ftp(fn) == efPDB) {
fp = gmx_ffopen(fn,"w");
if (bDiamond)
fprintf(fp,"HEADER This is a *diamond*\n");
else
fprintf(fp,"HEADER A beautiful Ice Ih crystal\n");
fprintf(fp,"REMARK Generated by mkice with the following options:\n"
"REMARK nx = %d, ny = %d, nz = %d, odist = %g, hdist = %g\n",
nx,ny,nz,odist,hdist);
bromacs(quote,255);
write_pdbfile(fp,quote,pdba,xx,boxje,' ',-1);
gmx_ffclose(fp);
}
else {
bromacs(quote,255);
write_sto_conf(fn,quote,pdba,xx,NULL,boxje);
}
if (ftp2bSet(efTRN,NFILE,fnm))
write_trn(ftp2fn(efTRN,NFILE,fnm),0,0,0,boxje,nmax,xx,NULL,NULL);
return 0;
}
int gmx_genion(int argc, char *argv[])
{
const char *desc[] = {
"[TT]genion[tt] replaces solvent molecules by monoatomic ions at",
"the position of the first atoms with the most favorable electrostatic",
"potential or at random. The potential is calculated on all atoms, using",
"normal GROMACS particle-based methods (in contrast to other methods",
"based on solving the Poisson-Boltzmann equation).",
"The potential is recalculated after every ion insertion.",
"If specified in the run input file, a reaction field, shift function",
"or user function can be used. For the user function a table file",
"can be specified with the option [TT]-table[tt].",
"The group of solvent molecules should be continuous and all molecules",
"should have the same number of atoms.",
"The user should add the ion molecules to the topology file or use",
"the [TT]-p[tt] option to automatically modify the topology.[PAR]",
"The ion molecule type, residue and atom names in all force fields",
"are the capitalized element names without sign. This molecule name",
"should be given with [TT]-pname[tt] or [TT]-nname[tt], and the",
"[TT][molecules][tt] section of your topology updated accordingly,",
"either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
"With the option [TT]-pot[tt] the potential can be written as B-factors",
"in a [TT].pdb[tt] file (for visualisation using e.g. Rasmol).",
"The unit of the potential is 1000 kJ/(mol e), the scaling be changed",
"with the [TT]-scale[tt] option.[PAR]",
"For larger ions, e.g. sulfate we recommended using [TT]genbox[tt]."
};
const char *bugs[] = {
"Calculation of the potential is not reliable, therefore the [TT]-random[tt] option is now turned on by default.",
"If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added."
};
static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
static const char *p_name = "NA", *n_name = "CL";
static real rmin = 0.6, scale = 0.001, conc = 0;
static int seed = 1993;
static gmx_bool bRandom = TRUE, bNeutral = FALSE;
static t_pargs pa[] = {
{ "-np", FALSE, etINT, {&p_num}, "Number of positive ions" },
{ "-pname", FALSE, etSTR, {&p_name}, "Name of the positive ion" },
{ "-pq", FALSE, etINT, {&p_q}, "Charge of the positive ion" },
{ "-nn", FALSE, etINT, {&n_num}, "Number of negative ions" },
{ "-nname", FALSE, etSTR, {&n_name}, "Name of the negative ion" },
{ "-nq", FALSE, etINT, {&n_q}, "Charge of the negative ion" },
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance between ions" },
{ "-random", FALSE, etBOOL, {&bRandom}, "Use random placement of ions instead of based on potential. The rmin option should still work" },
{ "-seed", FALSE, etINT, {&seed}, "Seed for random number generator" },
{ "-scale", FALSE, etREAL, {&scale}, "Scaling factor for the potential for [TT]-pot[tt]" },
{ "-conc", FALSE, etREAL, {&conc},
"Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [TT].tpr[tt] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
{ "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
};
gmx_mtop_t *mtop;
gmx_localtop_t *top;
t_inputrec inputrec;
t_commrec *cr;
t_mdatoms *mdatoms;
gmx_enerdata_t enerd;
t_graph *graph;
t_forcerec *fr;
rvec *x, *v;
real *pot, vol, qtot;
matrix box;
t_atoms atoms;
t_pbc pbc;
int *repl;
atom_id *index;
char *grpname;
gmx_bool *bSet, bPDB;
int i, nw, nwa, nsa, nsalt, iqtot;
FILE *fplog;
output_env_t oenv;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efXVG, "-table", "table", ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTO, "-o", NULL, ffWRITE },
{ efLOG, "-g", "genion", ffWRITE },
{ efPDB, "-pot", "pot", ffOPTWR },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bPDB = ftp2bSet(efPDB, NFILE, fnm);
if (bRandom && bPDB)
{
fprintf(stderr, "Not computing potential with random option!\n");
bPDB = FALSE;
}
/* Check input for something sensible */
if ((p_num < 0) || (n_num < 0))
{
gmx_fatal(FARGS, "Negative number of ions to add?");
}
snew(mtop, 1);
snew(top, 1);
fplog = init_calcpot(ftp2fn(efLOG, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm),
opt2fn("-table", NFILE, fnm), mtop, top, &inputrec, &cr,
&graph, &mdatoms, &fr, &enerd, &pot, box, &x, oenv);
atoms = gmx_mtop_global_atoms(mtop);
qtot = 0;
for (i = 0; (i < atoms.nr); i++)
{
qtot += atoms.atom[i].q;
}
iqtot = gmx_nint(qtot);
if (conc > 0)
{
/* Compute number of ions to be added */
vol = det(box);
nsalt = gmx_nint(conc*vol*AVOGADRO/1e24);
p_num = abs(nsalt*n_q);
n_num = abs(nsalt*p_q);
}
if (bNeutral)
{
int qdelta = p_num*p_q + n_num*n_q + iqtot;
/* Check if the system is neutralizable
* is (qdelta == p_q*p_num + n_q*n_num) solvable for p_num and n_num? */
int gcd = greatest_common_divisor(n_q, p_q);
if ((qdelta % gcd) != 0)
{
gmx_fatal(FARGS, "Can't neutralize this system using -nq %d and"
" -pq %d.\n", n_q, p_q);
}
while (qdelta != 0)
{
while (qdelta < 0)
{
p_num++;
qdelta += p_q;
}
while (qdelta > 0)
{
n_num++;
qdelta += n_q;
}
}
}
if ((p_num == 0) && (n_num == 0))
{
if (!bPDB)
{
fprintf(stderr, "No ions to add and no potential to calculate.\n");
exit(0);
}
nw = 0;
nsa = 0; /* to keep gcc happy */
}
else
{
printf("Will try to add %d %s ions and %d %s ions.\n",
p_num, p_name, n_num, n_name);
printf("Select a continuous group of solvent molecules\n");
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nwa, &index, &grpname);
for (i = 1; i < nwa; i++)
{
if (index[i] != index[i-1]+1)
{
gmx_fatal(FARGS, "The solvent group %s is not continuous: "
"index[%d]=%d, index[%d]=%d",
grpname, i, index[i-1]+1, i+1, index[i]+1);
}
}
nsa = 1;
while ((nsa < nwa) &&
(atoms.atom[index[nsa]].resind ==
atoms.atom[index[nsa-1]].resind))
{
nsa++;
}
if (nwa % nsa)
{
gmx_fatal(FARGS, "Your solvent group size (%d) is not a multiple of %d",
nwa, nsa);
}
nw = nwa/nsa;
fprintf(stderr, "Number of (%d-atomic) solvent molecules: %d\n", nsa, nw);
if (p_num+n_num > nw)
{
gmx_fatal(FARGS, "Not enough solvent for adding ions");
}
}
if (opt2bSet("-p", NFILE, fnm))
{
update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
}
snew(bSet, nw);
snew(repl, nw);
snew(v, atoms.nr);
snew(atoms.pdbinfo, atoms.nr);
set_pbc(&pbc, inputrec.ePBC, box);
/* Now loop over the ions that have to be placed */
do
{
if (!bRandom)
{
calc_pot(fplog, cr, mtop, &inputrec, top, x, fr, &enerd, mdatoms, pot, box, graph);
if (bPDB || debug)
{
char buf[STRLEN];
if (debug)
{
sprintf(buf, "%d_%s", p_num+n_num, ftp2fn(efPDB, NFILE, fnm));
}
else
{
strcpy(buf, ftp2fn(efPDB, NFILE, fnm));
}
for (i = 0; (i < atoms.nr); i++)
{
atoms.pdbinfo[i].bfac = pot[i]*scale;
}
write_sto_conf(buf, "Potential calculated by genion",
&atoms, x, v, inputrec.ePBC, box);
bPDB = FALSE;
}
}
if ((p_num > 0) && (p_num >= n_num))
{
insert_ion(nsa, &nw, bSet, repl, index, pot, x, &pbc,
1, p_q, p_name, mdatoms, rmin, bRandom, &seed);
p_num--;
}
else if (n_num > 0)
{
insert_ion(nsa, &nw, bSet, repl, index, pot, x, &pbc,
-1, n_q, n_name, mdatoms, rmin, bRandom, &seed);
n_num--;
}
}
while (p_num+n_num > 0);
fprintf(stderr, "\n");
if (nw)
{
sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
}
sfree(atoms.pdbinfo);
atoms.pdbinfo = NULL;
write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *mtop->name, &atoms, x, NULL,
inputrec.ePBC, box);
thanx(stderr);
gmx_log_close(fplog);
return 0;
}
int gmx_genconf(int argc, char *argv[])
{
const char *desc[] = {
"[TT]genconf[tt] multiplies a given coordinate file by simply stacking them",
"on top of each other, like a small child playing with wooden blocks.",
"The program makes a grid of [IT]user-defined[it]",
"proportions ([TT]-nbox[tt]), ",
"and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
"When option [TT]-rot[tt] is used the program does not check for overlap",
"between molecules on grid points. It is recommended to make the box in",
"the input file at least as big as the coordinates + ",
"van der Waals radius.[PAR]",
"If the optional trajectory file is given, conformations are not",
"generated, but read from this file and translated appropriately to",
"build the grid."
};
const char *bugs[] = {
"The program should allow for random displacement of lattice points."
};
int vol;
t_atoms *atoms; /* list with all atoms */
char title[STRLEN];
rvec *x, *xx, *v; /* coordinates? */
real t;
vec4 *xrot, *vrot;
int ePBC;
matrix box, boxx; /* box length matrix */
rvec shift;
int natoms; /* number of atoms in one molecule */
int nres; /* number of molecules? */
int i, j, k, l, m, ndx, nrdx, nx, ny, nz;
t_trxstatus *status;
gmx_bool bTRX;
output_env_t oenv;
t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efSTO, "-o", "out", ffWRITE },
{ efTRX, "-trj", NULL, ffOPTRD }
};
#define NFILE asize(fnm)
static rvec nrbox = {1, 1, 1};
static int seed = 0; /* seed for random number generator */
static int nmolat = 3;
static int nblock = 1;
static gmx_bool bShuffle = FALSE;
static gmx_bool bSort = FALSE;
static gmx_bool bRandom = FALSE; /* False: no random rotations */
static gmx_bool bRenum = TRUE; /* renumber residues */
static rvec dist = {0, 0, 0}; /* space added between molecules ? */
static rvec max_rot = {180, 180, 180}; /* maximum rotation */
t_pargs pa[] = {
{ "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
{ "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed, if 0 generated from the time" },
{ "-rot", FALSE, etBOOL, {&bRandom}, "Randomly rotate conformations" },
{ "-shuffle", FALSE, etBOOL, {&bShuffle}, "Random shuffling of molecules" },
{ "-sort", FALSE, etBOOL, {&bSort}, "Sort molecules on X coord" },
{ "-block", FALSE, etINT, {&nblock},
"Divide the box in blocks on this number of cpus" },
{ "-nmolat", FALSE, etINT, {&nmolat},
"Number of atoms per molecule, assumed to start from 0. "
"If you set this wrong, it will screw up your system!" },
{ "-maxrot", FALSE, etRVEC, {max_rot}, "Maximum random rotation" },
{ "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
};
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
if (bRandom && (seed == 0))
{
seed = make_seed();
}
bTRX = ftp2bSet(efTRX, NFILE, fnm);
nx = (int)(nrbox[XX]+0.5);
ny = (int)(nrbox[YY]+0.5);
nz = (int)(nrbox[ZZ]+0.5);
if ((nx <= 0) || (ny <= 0) || (nz <= 0))
{
gmx_fatal(FARGS, "Number of boxes (-nbox) should be larger than zero");
}
if ((nmolat <= 0) && bShuffle)
{
gmx_fatal(FARGS, "Can not shuffle if the molecules only have %d atoms",
nmolat);
}
vol = nx*ny*nz; /* calculate volume in grid points (= nr. molecules) */
get_stx_coordnum(opt2fn("-f", NFILE, fnm), &natoms);
snew(atoms, 1);
/* make space for all the atoms */
init_t_atoms(atoms, natoms*vol, FALSE);
snew(x, natoms*vol); /* get space for coordinates of all atoms */
snew(xrot, natoms); /* get space for rotation matrix? */
snew(v, natoms*vol); /* velocities. not really needed? */
snew(vrot, natoms);
/* set atoms->nr to the number in one box *
* to avoid complaints in read_stx_conf *
*/
atoms->nr = natoms;
read_stx_conf(opt2fn("-f", NFILE, fnm), title, atoms, x, v, &ePBC, box);
nres = atoms->nres; /* nr of residues in one element? */
if (bTRX)
{
if (!read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &xx, boxx))
{
gmx_fatal(FARGS, "No atoms in trajectory %s", ftp2fn(efTRX, NFILE, fnm));
}
}
else
{
snew(xx, natoms);
for (i = 0; i < natoms; i++)
{
copy_rvec(x[i], xx[i]);
}
}
for (k = 0; (k < nz); k++) /* loop over all gridpositions */
{
shift[ZZ] = k*(dist[ZZ]+box[ZZ][ZZ]);
for (j = 0; (j < ny); j++)
{
shift[YY] = j*(dist[YY]+box[YY][YY])+k*box[ZZ][YY];
for (i = 0; (i < nx); i++)
{
shift[XX] = i*(dist[XX]+box[XX][XX])+j*box[YY][XX]+k*box[ZZ][XX];
ndx = (i*ny*nz+j*nz+k)*natoms;
nrdx = (i*ny*nz+j*nz+k)*nres;
/* Random rotation on input coords */
if (bRandom)
{
rand_rot(natoms, xx, v, xrot, vrot, &seed, max_rot);
}
for (l = 0; (l < natoms); l++)
{
for (m = 0; (m < DIM); m++)
{
if (bRandom)
{
x[ndx+l][m] = xrot[l][m];
v[ndx+l][m] = vrot[l][m];
}
else
{
x[ndx+l][m] = xx[l][m];
v[ndx+l][m] = v[l][m];
}
}
if (ePBC == epbcSCREW && i % 2 == 1)
{
/* Rotate around x axis */
for (m = YY; m <= ZZ; m++)
{
x[ndx+l][m] = box[YY][m] + box[ZZ][m] - x[ndx+l][m];
v[ndx+l][m] = -v[ndx+l][m];
}
}
for (m = 0; (m < DIM); m++)
{
x[ndx+l][m] += shift[m];
}
atoms->atom[ndx+l].resind = nrdx + atoms->atom[l].resind;
atoms->atomname[ndx+l] = atoms->atomname[l];
}
for (l = 0; (l < nres); l++)
{
atoms->resinfo[nrdx+l] = atoms->resinfo[l];
if (bRenum)
{
atoms->resinfo[nrdx+l].nr += nrdx;
}
}
if (bTRX)
{
if (!read_next_x(oenv, status, &t, natoms, xx, boxx) &&
((i+1)*(j+1)*(k+1) < vol))
{
gmx_fatal(FARGS, "Not enough frames in trajectory");
}
}
}
}
}
if (bTRX)
{
close_trj(status);
}
/* make box bigger */
for (m = 0; (m < DIM); m++)
{
box[m][m] += dist[m];
}
svmul(nx, box[XX], box[XX]);
svmul(ny, box[YY], box[YY]);
svmul(nz, box[ZZ], box[ZZ]);
if (ePBC == epbcSCREW && nx % 2 == 0)
{
/* With an even number of boxes in x we can forgot about the screw */
ePBC = epbcXYZ;
}
/* move_x(natoms*vol,x,box); */ /* put atoms in box? */
atoms->nr *= vol;
atoms->nres *= vol;
/*depending on how you look at it, this is either a nasty hack or the way it should work*/
if (bRenum)
{
for (i = 0; i < atoms->nres; i++)
{
atoms->resinfo[i].nr = i+1;
}
}
if (bShuffle)
{
randwater(0, atoms->nr/nmolat, nmolat, x, v, &seed);
}
else if (bSort)
{
sortwater(0, atoms->nr/nmolat, nmolat, x, v);
}
else if (opt2parg_bSet("-block", asize(pa), pa))
{
mkcompact(0, atoms->nr/nmolat, nmolat, x, v, nblock, box);
}
write_sto_conf(opt2fn("-o", NFILE, fnm), title, atoms, x, v, ePBC, box);
thanx(stderr);
return 0;
}
int gmx_helix(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes all kinds of helix properties. First, the peptide",
"is checked to find the longest helical part, as determined by",
"hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
"That bit is fitted",
"to an ideal helix around the [IT]z[it]-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file [TT]radius.xvg[tt]). This is merely the",
"RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
"it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file [TT]twist.xvg[tt]). The average helical angle per",
"residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
"for 3-10 helices it will be smaller, and ",
"for 5-helices it will be larger.[BR]",
"[BB]3.[bb] Rise per residue (file [TT]rise.xvg[tt]). The helical rise per",
"residue is plotted as the difference in [IT]z[it]-coordinate between C[GRK]alpha[grk]",
"atoms. For an ideal helix, this is 0.15 nm[BR]",
"[BB]4.[bb] Total helix length (file [TT]len-ahx.xvg[tt]). The total length",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"number of helical residues (see below).[BR]",
"[BB]5.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
"[BB]6.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
"atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
"[BB]7.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
"[BB]8.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
"[BB]9.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
"[PAR]"
};
static gmx_bool bCheck = FALSE, bFit = TRUE, bDBG = FALSE, bEV = FALSE;
static int rStart = 0, rEnd = 0, r0 = 1;
t_pargs pa [] = {
{ "-r0", FALSE, etINT, {&r0},
"The first residue number in the sequence" },
{ "-q", FALSE, etBOOL, {&bCheck},
"Check at every step which part of the sequence is helical" },
{ "-F", FALSE, etBOOL, {&bFit},
"Toggle fit to a perfect helix" },
{ "-db", FALSE, etBOOL, {&bDBG},
"Print debug info" },
{ "-ev", FALSE, etBOOL, {&bEV},
"Write a new 'trajectory' file for ED" },
{ "-ahxstart", FALSE, etINT, {&rStart},
"First residue in helix" },
{ "-ahxend", FALSE, etINT, {&rEnd},
"Last residue in helix" }
};
typedef struct {
FILE *fp, *fp2;
gmx_bool bfp2;
const char *filenm;
const char *title;
const char *xaxis;
const char *yaxis;
real val;
} t_xvgrfile;
t_xvgrfile xf[efhNR] = {
{ NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)", 0.0 },
{ NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 },
{ NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 },
{ NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 },
{ NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 },
{ NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "rmsa-ahx", "Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg", 0.0 },
{ NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 },
{ NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg", 0.0 },
{ NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg", 0.0 },
{ NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm", 0.0 },
{ NULL, NULL, FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz", 0.0 },
{ NULL, NULL, FALSE, "helicity", "Helicity per Residue", "Residue", "% of time", 0.0 }
};
output_env_t oenv;
char buf[54];
t_trxstatus *status;
int natoms, nre, nres;
t_bb *bb;
int i, j, m, nall, nbb, nca, teller, nSel = 0;
atom_id *bbindex, *caindex, *allindex;
t_topology *top;
int ePBC;
rvec *x, *xref;
real t;
real rms;
matrix box;
gmx_rmpbc_t gpbc = NULL;
gmx_bool bRange;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efSTO, "-cz", "zconf", ffWRITE },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
opt2parg_bSet("-ahxend", asize(pa), pa));
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
natoms = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
if (natoms != top->atoms.nr)
{
gmx_fatal(FARGS, "Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
top->atoms.nr, natoms);
}
bb = mkbbind(ftp2fn(efNDX, NFILE, fnm), &nres, &nbb, r0, &nall, &allindex,
top->atoms.atomname, top->atoms.atom, top->atoms.resinfo);
snew(bbindex, natoms);
snew(caindex, nres);
fprintf(stderr, "nall=%d\n", nall);
/* Open output files, default x-axis is time */
for (i = 0; (i < efhNR); i++)
{
sprintf(buf, "%s.xvg", xf[i].filenm);
remove(buf);
xf[i].fp = xvgropen(buf, xf[i].title,
xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
xf[i].yaxis, oenv);
if (xf[i].bfp2)
{
sprintf(buf, "%s.out", xf[i].filenm);
remove(buf);
xf[i].fp2 = gmx_ffopen(buf, "w");
}
}
/* Read reference frame from tpx file to compute helix length */
snew(xref, top->atoms.nr);
read_tpx(ftp2fn(efTPX, NFILE, fnm),
NULL, NULL, &natoms, xref, NULL, NULL, NULL);
calc_hxprops(nres, bb, xref);
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
sfree(xref);
if (bDBG)
{
fprintf(stderr, "nca=%d, nbb=%d\n", nca, nbb);
pr_bb(stdout, nres, bb);
}
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
teller = 0;
do
{
if ((teller++ % 10) == 0)
{
fprintf(stderr, "\rt=%.2f", t);
}
gmx_rmpbc(gpbc, natoms, box, x);
calc_hxprops(nres, bb, x);
if (bCheck)
{
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, FALSE, 0, 0);
}
if (nca >= 5)
{
rms = fit_ahx(nres, bb, natoms, nall, allindex, x, nca, caindex, bFit);
if (teller == 1)
{
write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis",
&(top->atoms), x, NULL, ePBC, box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2, nca, caindex, x);
xf[efhTWIST].val = twist(nca, caindex, x);
xf[efhRISE].val = rise(nca, caindex, x);
xf[efhLEN].val = ahx_len(nca, caindex, x);
xf[efhCD222].val = ellipticity(nres, bb);
xf[efhDIP].val = dip(nbb, bbindex, x, top->atoms.atom);
xf[efhRMS].val = rms;
xf[efhCPHI].val = ca_phi(nca, caindex, x);
xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2, nres, bb);
for (j = 0; (j <= efhCPHI); j++)
{
fprintf(xf[j].fp, "%10g %10g\n", t, xf[j].val);
}
av_phipsi(xf[efhPHI].fp, xf[efhPSI].fp, xf[efhPHI].fp2, xf[efhPSI].fp2,
t, nres, bb);
av_hblen(xf[efhHB3].fp, xf[efhHB3].fp2,
xf[efhHB4].fp, xf[efhHB4].fp2,
xf[efhHB5].fp, xf[efhHB5].fp2,
t, nres, bb);
}
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
gmx_rmpbc_done(gpbc);
close_trj(status);
for (i = 0; (i < nres); i++)
{
if (bb[i].nrms > 0)
{
fprintf(xf[efhRMSA].fp, "%10d %10g\n", r0+i, bb[i].rmsa/bb[i].nrms);
}
fprintf(xf[efhAHX].fp, "%10d %10g\n", r0+i, (bb[i].nhx*100.0)/(real )teller);
fprintf(xf[efhJCA].fp, "%10d %10g\n",
r0+i, 140.3+(bb[i].jcaha/(double)teller));
}
for (i = 0; (i < efhNR); i++)
{
gmx_ffclose(xf[i].fp);
if (xf[i].bfp2)
{
gmx_ffclose(xf[i].fp2);
}
do_view(oenv, xf[i].filenm, "-nxy");
}
return 0;
}
int gmx_editconf(int argc, char *argv[])
{
const char
*desc[] =
{
"editconf converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"will center the system in the box, unless [TT]-noc[tt] is used.",
"[PAR]",
"Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
"triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
"[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
"[TT]octahedron[tt] is a truncated octahedron.",
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
"The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
"is 0.77 of that of a cubic box with the same periodic image distance.",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic box, dodecahedron and a truncated octahedron.",
"[PAR]",
"With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
"and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
"a triclinic box and can not be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"otherwise the whole system is used.",
"[PAR]",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
"coordinate axes, this may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the plains, when one uses -1 in three dimensions",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
"It is important that the box sizes at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
"When writing [TT].pdb[tt] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
"unless an index is larger than the number of residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
"With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
"The option -grasp is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Option [TT]-align[tt] allows alignment",
"of the principal axis of a specified group against the given vector, ",
"with an optional center of rotation specified by [TT]-aligncenter[tt].",
"[PAR]",
"Finally with option [TT]-label[tt] editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol.",
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as Gromos) use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
const char *bugs[] =
{
"For complex molecules, the periodicity removal routine may break down, ",
"in that case you can use trjconv." };
static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
FALSE, bCONECT = FALSE;
static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
FALSE, bGrasp = FALSE, bSig56 = FALSE;
static rvec scale =
{ 1, 1, 1 }, newbox =
{ 0, 0, 0 }, newang =
{ 90, 90, 90 };
static real rho = 1000.0, rvdw = 0.12;
static rvec center =
{ 0, 0, 0 }, translation =
{ 0, 0, 0 }, rotangles =
{ 0, 0, 0 }, aligncenter =
{ 0, 0, 0 }, targetvec =
{ 0, 0, 0 };
static const char *btype[] =
{ NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
*label = "A";
static rvec visbox =
{ 0, 0, 0 };
t_pargs
pa[] =
{
{ "-ndef", FALSE, etBOOL,
{ &bNDEF }, "Choose output from default index groups" },
{ "-visbox", FALSE, etRVEC,
{ visbox },
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
{ "-bt", FALSE, etENUM,
{ btype }, "Box type for -box and -d" },
{ "-box", FALSE, etRVEC,
{ newbox }, "Box vector lengths (a,b,c)" },
{ "-angles", FALSE, etRVEC,
{ newang }, "Angles between the box vectors (bc,ac,ab)" },
{ "-d", FALSE, etREAL,
{ &dist }, "Distance between the solute and the box" },
{ "-c", FALSE, etBOOL,
{ &bCenter },
"Center molecule in box (implied by -box and -d)" },
{ "-center", FALSE, etRVEC,
{ center }, "Coordinates of geometrical center" },
{ "-aligncenter", FALSE, etRVEC,
{ aligncenter }, "Center of rotation for alignment" },
{ "-align", FALSE, etRVEC,
{ targetvec },
"Align to target vector" },
{ "-translate", FALSE, etRVEC,
{ translation }, "Translation" },
{ "-rotate", FALSE, etRVEC,
{ rotangles },
"Rotation around the X, Y and Z axes in degrees" },
{ "-princ", FALSE, etBOOL,
{ &bOrient },
"Orient molecule(s) along their principal axes" },
{ "-scale", FALSE, etRVEC,
{ scale }, "Scaling factor" },
{ "-density", FALSE, etREAL,
{ &rho },
"Density (g/l) of the output box achieved by scaling" },
{ "-pbc", FALSE, etBOOL,
{ &bRMPBC },
"Remove the periodicity (make molecule whole again)" },
{ "-grasp", FALSE, etBOOL,
{ &bGrasp },
"Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
{
"-rvdw", FALSE, etREAL,
{ &rvdw },
"Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
{ "-sig56", FALSE, etREAL,
{ &bSig56 },
"Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
{
"-vdwread", FALSE, etBOOL,
{ &bReadVDW },
"Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
{ "-atom", FALSE, etBOOL,
{ &peratom }, "Force B-factor attachment per atom" },
{ "-legend", FALSE, etBOOL,
{ &bLegend }, "Make B-factor legend" },
{ "-label", FALSE, etSTR,
{ &label }, "Add chain label for all residues" },
{
"-conect", FALSE, etBOOL,
{ &bCONECT },
"Add CONECT records to a pdb file when written. Can only be done when a topology is present" } };
#define NPA asize(pa)
FILE *out;
const char *infile, *outfile;
char title[STRLEN];
int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
double *bfac = NULL, c6, c12;
int *bfac_nr = NULL;
t_topology *top = NULL;
t_atoms atoms;
char *grpname, *sgrpname, *agrpname;
int isize, ssize, tsize, asize;
atom_id *index, *sindex, *tindex, *aindex;
rvec *x, *v, gc, min, max, size;
int ePBC;
matrix box,rotmatrix,trans;
rvec princd,tmpvec;
gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
gmx_atomprop_t aps;
gmx_conect conect;
output_env_t oenv;
t_filenm fnm[] =
{
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efSTO, NULL, NULL, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
bMead = opt2bSet("-mead", NFILE, fnm);
bSetSize = opt2parg_bSet("-box", NPA, pa);
bSetAng = opt2parg_bSet("-angles", NPA, pa);
bSetCenter = opt2parg_bSet("-center", NPA, pa);
bDist = opt2parg_bSet("-d", NPA, pa);
bAlign = opt2parg_bSet("-align", NPA, pa);
/* Only automatically turn on centering without -noc */
if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
{
bCenter = TRUE;
}
bScale = opt2parg_bSet("-scale", NPA, pa);
bRho = opt2parg_bSet("-density", NPA, pa);
bTranslate = opt2parg_bSet("-translate", NPA, pa);
bRotate = opt2parg_bSet("-rotate", NPA, pa);
if (bScale && bRho)
fprintf(stderr, "WARNING: setting -density overrides -scale\n");
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';
infile = ftp2fn(efSTX, NFILE, fnm);
if (bMead)
outfile = ftp2fn(efPQR, NFILE, fnm);
else
outfile = ftp2fn(efSTO, NFILE, fnm);
outftp = fn2ftp(outfile);
inftp = fn2ftp(infile);
aps = gmx_atomprop_init();
if (bMead && bGrasp)
{
printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
bGrasp = FALSE;
}
if (bGrasp && (outftp != efPDB))
gmx_fatal(FARGS, "Output file should be a .pdb file"
" when using the -grasp option\n");
if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
(fn2ftp(infile) == efTPA) ||
(fn2ftp(infile) == efTPB)))
gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
" when using the -mead option\n");
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(x,natom);
snew(v,natom);
read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
if (fn2ftp(infile) == efPDB)
{
get_pdb_atomnumber(&atoms,aps);
}
printf("Read %d atoms\n",atoms.nr);
/* Get the element numbers if available in a pdb file */
if (fn2ftp(infile) == efPDB)
get_pdb_atomnumber(&atoms,aps);
if (ePBC != epbcNONE)
{
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
vol,100*((int)(vol*4.5)));
}
if (bMead || bGrasp || bCONECT)
top = read_top(infile,NULL);
if (bMead || bGrasp)
{
if (atoms.nr != top->atoms.nr)
gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",atoms.nr,top->atoms.nr);
snew(atoms.pdbinfo,top->atoms.nr);
ntype = top->idef.atnr;
for(i=0; (i<atoms.nr); i++) {
/* Determine the Van der Waals radius from the force field */
if (bReadVDW) {
if (!gmx_atomprop_query(aps,epropVDW,
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i],&vdw))
vdw = rvdw;
}
else {
itype = top->atoms.atom[i].type;
c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
if ((c6 != 0) && (c12 != 0)) {
real sig6;
if (bSig56)
sig6 = 2*c12/c6;
else
sig6 = c12/c6;
vdw = 0.5*pow(sig6,1.0/6.0);
}
else
vdw = rvdw;
}
/* Factor of 10 for nm -> Angstroms */
vdw *= 10;
if (bMead) {
atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
atoms.pdbinfo[i].bfac = vdw;
}
else {
atoms.pdbinfo[i].occup = vdw;
atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
}
}
}
bHaveV=FALSE;
for (i=0; (i<natom) && !bHaveV; i++)
for (j=0; (j<DIM) && !bHaveV; j++)
bHaveV=bHaveV || (v[i][j]!=0);
printf("%selocities found\n",bHaveV?"V":"No v");
if (visbox[0] > 0) {
if (bIndex)
gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
if (outftp != efPDB)
gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
} else if (visbox[0] == -1)
visualize_images("images.pdb",ePBC,box);
/* remove pbc */
if (bRMPBC)
rm_gropbc(&atoms,x,box);
if (bCalcGeom) {
if (bIndex) {
fprintf(stderr,"\nSelect a group for determining the system size:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
rvec_sub(max, min, size);
printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
printf(" diameter :%7.3f (nm)\n",diam);
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf(" box volume :%7.2f (nm^3)\n",det(box));
}
if (bRho || bOrient || bAlign)
mass = calc_mass(&atoms,!fn2bTPX(infile),aps);
if (bOrient) {
atom_id *index;
char *grpnames;
/* Get a group for principal component analysis */
fprintf(stderr,"\nSelect group for the determining the orientation\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Orient the principal axes along the coordinate axes */
orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
sfree(index);
sfree(grpnames);
}
if ( bScale ) {
/* scale coordinates and box */
if (bRho) {
/* Compute scaling constant */
real vol,dens;
vol = det(box);
dens = (mass*AMU)/(vol*NANO*NANO*NANO);
fprintf(stderr,"Volume of input %g (nm^3)\n",vol);
fprintf(stderr,"Mass of input %g (a.m.u.)\n",mass);
fprintf(stderr,"Density of input %g (g/l)\n",dens);
if (vol==0 || mass==0)
gmx_fatal(FARGS,"Cannot scale density with "
"zero mass (%g) or volume (%g)\n",mass,vol);
scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
}
scale_conf(atoms.nr,x,box,scale);
}
if (bAlign) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to align:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&asize,&aindex,&agrpname);
} else {
asize = atoms.nr;
snew(aindex,asize);
for (i=0;i<asize;i++)
aindex[i]=i;
}
printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",asize,natom,
targetvec[XX],targetvec[YY],targetvec[ZZ],
aligncenter[XX],aligncenter[YY],aligncenter[ZZ]);
/*subtract out pivot point*/
for(i=0; i<asize; i++)
rvec_dec(x[aindex[i]],aligncenter);
/*now determine transform and rotate*/
/*will this work?*/
principal_comp(asize,aindex,atoms.atom,x, trans,princd);
unitv(targetvec,targetvec);
printf("Using %g %g %g as principal axis\n", trans[0][2],trans[1][2],trans[2][2]);
tmpvec[XX]=trans[0][2]; tmpvec[YY]=trans[1][2]; tmpvec[ZZ]=trans[2][2];
calc_rotmatrix(tmpvec, targetvec, rotmatrix);
/* rotmatrix finished */
for (i=0;i<asize;++i)
{
mvmul(rotmatrix,x[aindex[i]],tmpvec);
copy_rvec(tmpvec,x[aindex[i]]);
}
/*add pivot point back*/
for(i=0; i<asize; i++)
rvec_inc(x[aindex[i]],aligncenter);
if (!bIndex)
sfree(aindex);
}
if (bTranslate) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to translate:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
printf("Translating %d atoms (out of %d) by %g %g %g nm\n",ssize,natom,
translation[XX],translation[YY],translation[ZZ]);
if (sindex) {
for(i=0; i<ssize; i++)
rvec_inc(x[sindex[i]],translation);
}
else {
for(i=0; i<natom; i++)
rvec_inc(x[i],translation);
}
}
if (bRotate) {
/* Rotate */
printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<DIM; i++)
rotangles[i] *= DEG2RAD;
rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
}
if (bCalcGeom) {
/* recalc geometrical center and max and min coordinates and size */
calc_geom(ssize,sindex,x,gc,min,max,FALSE);
rvec_sub(max, min, size);
if (bScale || bOrient || bRotate)
printf("new system size : %6.3f %6.3f %6.3f\n",
size[XX],size[YY],size[ZZ]);
}
if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
for (i=0; i<DIM; i++)
newbox[i] = norm(box[i]);
clear_mat(box);
/* calculate new boxsize */
switch(btype[0][0]){
case 't':
if (bDist)
for(i=0; i<DIM; i++)
newbox[i] = size[i]+2*dist;
if (!bSetAng) {
box[XX][XX] = newbox[XX];
box[YY][YY] = newbox[YY];
box[ZZ][ZZ] = newbox[ZZ];
} else {
matrix_convert(box,newbox,newang);
}
break;
case 'c':
case 'd':
case 'o':
if (bSetSize)
d = newbox[0];
else
d = diam+2*dist;
if (btype[0][0] == 'c')
for(i=0; i<DIM; i++)
box[i][i] = d;
else if (btype[0][0] == 'd') {
box[XX][XX] = d;
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
box[ZZ][ZZ] = d*sqrt(2)/2;
} else {
box[XX][XX] = d;
box[YY][XX] = d/3;
box[YY][YY] = d*sqrt(2)*2/3;
box[ZZ][XX] = -d/3;
box[ZZ][YY] = d*sqrt(2)/3;
box[ZZ][ZZ] = d*sqrt(6)/3;
}
break;
}
}
/* calculate new coords for geometrical center */
if (!bSetCenter)
calc_box_center(ecenterDEF,box,center);
/* center molecule on 'center' */
if (bCenter)
center_conf(natom,x,center,gc);
/* print some */
if (bCalcGeom) {
calc_geom(ssize,sindex,x, gc, min, max, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
}
if (bOrient || bScale || bDist || bSetSize) {
printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(box))
{
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
"You can check the actual value with g_mindist -pi\n",dist);
}
else
{
printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
}
if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
conect = gmx_conect_generate(top);
else
conect = NULL;
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
if (opt2bSet("-bf",NFILE,fnm) || bLegend)
{
gmx_fatal(FARGS,"Sorry, cannot do bfactors with an index group.");
}
if (outftp == efPDB)
{
out=ffopen(outfile,"w");
write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect,TRUE);
ffclose(out);
}
else
{
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,isize,index);
}
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp) {
fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
fprintf(out,"REMARK "
"The B-factors in this file hold atomic charges\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf",NFILE,fnm)) {
read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
n_bfac,bfac,bfac_nr,peratom);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,' ',-1,conect,TRUE);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
ffclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(oenv,outfile,NULL);
thanx(stderr);
return 0;
}
void printmol(t_corr *curr, const char *fn,
const char *fn_pdb, int *molindex, t_topology *top,
rvec *x, int ePBC, matrix box, const output_env_t oenv)
{
#define NDIST 100
FILE *out;
gmx_stats_t lsq1;
int i, j;
real a, b, D, Dav, D2av, VarD, sqrtD, sqrtD_max, scale;
t_pdbinfo *pdbinfo = NULL;
int *mol2a = NULL;
out = xvgropen(fn, "Diffusion Coefficients / Molecule", "Molecule", "D", oenv);
if (fn_pdb)
{
if (top->atoms.pdbinfo == NULL)
{
snew(top->atoms.pdbinfo, top->atoms.nr);
}
pdbinfo = top->atoms.pdbinfo;
mol2a = top->mols.index;
}
Dav = D2av = 0;
sqrtD_max = 0;
for (i = 0; (i < curr->nmol); i++)
{
lsq1 = gmx_stats_init();
for (j = 0; (j < curr->nrestart); j++)
{
real xx, yy, dx, dy;
while (gmx_stats_get_point(curr->lsq[j][i], &xx, &yy, &dx, &dy, 0) == estatsOK)
{
gmx_stats_add_point(lsq1, xx, yy, dx, dy);
}
}
gmx_stats_get_ab(lsq1, elsqWEIGHT_NONE, &a, &b, NULL, NULL, NULL, NULL);
gmx_stats_done(lsq1);
sfree(lsq1);
D = a*FACTOR/curr->dim_factor;
if (D < 0)
{
D = 0;
}
Dav += D;
D2av += sqr(D);
fprintf(out, "%10d %10g\n", i, D);
if (pdbinfo)
{
sqrtD = std::sqrt(D);
if (sqrtD > sqrtD_max)
{
sqrtD_max = sqrtD;
}
for (j = mol2a[molindex[i]]; j < mol2a[molindex[i]+1]; j++)
{
pdbinfo[j].bfac = sqrtD;
}
}
}
xvgrclose(out);
do_view(oenv, fn, "-graphtype bar");
/* Compute variance, stddev and error */
Dav /= curr->nmol;
D2av /= curr->nmol;
VarD = D2av - sqr(Dav);
printf("<D> = %.4f Std. Dev. = %.4f Error = %.4f\n",
Dav, std::sqrt(VarD), std::sqrt(VarD/curr->nmol));
if (fn_pdb && x)
{
scale = 1;
while (scale*sqrtD_max > 10)
{
scale *= 0.1;
}
while (scale*sqrtD_max < 0.1)
{
scale *= 10;
}
GMX_RELEASE_ASSERT(pdbinfo != NULL, "Internal error - pdbinfo not set for PDB input");
for (i = 0; i < top->atoms.nr; i++)
{
pdbinfo[i].bfac *= scale;
}
write_sto_conf(fn_pdb, "molecular MSD", &top->atoms, x, NULL, ePBC, box);
}
}
int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]do_multiprot[tt] ",
"reads a trajectory file and aligns it to a reference structure ",
"each time frame",
"calling the multiprot program. This allows you to use a reference",
"structure whose sequence is different than that of the protein in the ",
"trajectory, since the alignment is based on the geometry, not sequence.",
"The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
"on which it was calculated.",
"[PAR]",
"An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
"With the [TT]-cr[tt] option, the number of hits in the alignment is given",
"per residue. This number can be between 0 and the number of frames, and",
"indicates the structural conservation of this residue.[PAR]",
"If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
"that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
"not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
"pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
"[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
"Note that at the current implementation only binary alignment (your",
"molecule to a reference) is supported. In addition, note that the ",
"by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
"and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
"with here. Thus, the C-alpha carbons is expected to give the same "
"results as choosing the whole protein and will be slightly faster.[PAR]",
"For information about [TT]multiprot[tt], see:",
"http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
};
static bool bVerbose;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" }
};
const char *bugs[] = {
"The program is very slow, since multiprot is run externally"
};
t_trxstatus *status;
t_trxstatus *trxout=NULL;
FILE *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
const char *fnRef;
const char *fn="2_sol.res";
t_topology top;
int ePBC;
t_atoms *atoms,ratoms,useatoms;
t_trxframe fr;
t_pdbinfo p;
int nres,nres2,nr0;
real t;
int i,j,natoms,nratoms,nframe=0,model_nr=-1;
int cur_res,prev_res;
int nout;
t_countres *countres=NULL;
matrix box,rbox;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x,*xr;
char pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
char out_title[256];
char multiprot[256],*mptr;
int ftp;
int outftp=-1;
real rmsd;
bool bTrjout,bCountres;
const char *TrjoutFile=NULL;
output_env_t oenv;
static rvec translation={0,0,0},rotangles={0,0,0};
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-r", NULL , ffREAD },
{ efXVG, "-o", "rmss", ffWRITE },
{ efXVG, "-rc", "rescount", ffWRITE},
{ efXVG, "-cr", "countres", ffOPTWR},
{ efTRX, "-ox", "aligned", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
fnRef=opt2fn("-r",NFILE,fnm);
bTrjout = opt2bSet("-ox",NFILE,fnm);
bCountres= opt2bSet("-cr",NFILE,fnm);
if (bTrjout) {
TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
atoms=&(top.atoms);
ftp=fn2ftp(fnRef);
get_stx_coordnum(fnRef,&nratoms);
init_t_atoms(&ratoms,nratoms,TRUE);
snew(xr,nratoms);
read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
if (bVerbose) {
fprintf(stderr,"Read %d atoms\n",atoms->nr);
fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
}
if (bCountres) {
snew(countres,ratoms.nres);
j=0;
cur_res=0;
for (i=0;i<ratoms.nr;i++) {
prev_res=cur_res;
cur_res=ratoms.atom[i].resind;
if (cur_res != prev_res) {
countres[j].resnr=cur_res;
countres[j].count=0;
j++;
}
}
}
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
nr0=-1;
for(i=0; (i<gnx); i++) {
if (atoms->atom[index[i]].resind != nr0) {
nr0=atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr,"There are %d residues in your selected group\n",nres);
strcpy(pdbfile,"ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
}
}
else {
gmx_ffclose(tmpf);
}
if (ftp != efPDB) {
strcpy(refpdb,"ddXXXXXX");
gmx_tmpnam(refpdb);
strcat(refpdb,".pdb");
write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
}
else {
strcpy(refpdb,fnRef);
}
if ((mptr=getenv("MULTIPROT")) == NULL) {
mptr="/usr/local/bin/multiprot";
}
if (!gmx_fexist(mptr)) {
gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
mptr);
}
sprintf (multiprot,"%s %s %s > /dev/null %s",
mptr, refpdb, pdbfile, "2> /dev/null");
if (bVerbose)
fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
natoms = fr.natoms;
if (bTrjout) {
nout=natoms;
/* open file now */
outftp=fn2ftp(TrjoutFile);
if (bVerbose)
fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
strcpy(filemode,"w");
switch (outftp) {
case efXTC:
case efG87:
case efTRR:
case efTRJ:
out=NULL;
trxout = open_trx(TrjoutFile,filemode);
break;
case efGRO:
case efG96:
case efPDB:
/* Make atoms struct for output in GRO or PDB files */
/* get memory for stuff to go in pdb file */
init_t_atoms(&useatoms,nout,FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo=atoms->resinfo;
for(i=0;(i<nout);i++) {
useatoms.atomname[i]=atoms->atomname[i];
useatoms.atom[i]=atoms->atom[i];
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
}
useatoms.nr=nout;
out=gmx_ffopen(TrjoutFile,filemode);
break;
}
}
if (natoms > atoms->nr) {
gmx_fatal(FARGS,"\nTrajectory does not match topology!");
}
if (gnx > natoms) {
gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
}
fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
do {
t = output_env_conv_time(oenv,fr.time);
gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
tapein=gmx_ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
gmx_ffclose(tapein);
system(multiprot);
remove(pdbfile);
process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
fprintf(fo,"%12.7f",t);
fprintf(fo," %12.7f\n",rmsd);
fprintf(frc,"%12.7f",t);
fprintf(frc,"%12d\n",nres2);
if (bTrjout) {
rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<natoms; i++) {
rvec_inc(fr.x[i],translation);
}
switch(outftp) {
case efTRJ:
case efTRR:
case efG87:
case efXTC:
write_trxframe(trxout,&fr,NULL);
break;
case efGRO:
case efG96:
case efPDB:
sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
switch(outftp) {
case efGRO:
write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
fr.x,NULL,fr.box);
break;
case efPDB:
fprintf(out,"REMARK GENERATED BY DO_MULTIPROT\n");
sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
/* if reading from pdb, we want to keep the original
model numbering else we write the output frame
number plus one, because model 0 is not allowed in pdb */
if (ftp==efPDB && fr.step > model_nr) {
model_nr = fr.step;
}
else {
model_nr++;
}
write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
break;
case efG96:
fr.title = out_title;
fr.bTitle = (nframe == 0);
fr.bAtoms = FALSE;
fr.bStep = TRUE;
fr.bTime = TRUE;
write_g96_conf(out,&fr,-1,NULL);
}
break;
}
}
nframe++;
} while(read_next_frame(oenv,status,&fr));
if (bCountres) {
fres= xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
for (i=0;i<ratoms.nres;i++) {
fprintf(fres,"%10d %12d\n",countres[i].resnr,countres[i].count);
}
gmx_ffclose(fres);
}
gmx_ffclose(fo);
gmx_ffclose(frc);
fprintf(stderr,"\n");
close_trj(status);
if (trxout != NULL) {
close_trx(trxout);
}
else if (out != NULL) {
gmx_ffclose(out);
}
view_all(oenv,NFILE, fnm);
sfree(xr);
if (bCountres) {
sfree(countres);
}
free_t_atoms(&ratoms,TRUE);
if (bTrjout) {
if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
free_t_atoms(&useatoms,TRUE);
}
}
gmx_thanx(stderr);
return 0;
}
void connelly_plot(const char *fn,int ndots,real dots[],rvec x[],t_atoms *atoms,
t_symtab *symtab,int ePBC,matrix box,gmx_bool bSave)
{
static const char *atomnm="DOT";
static const char *resnm ="DOT";
static const char *title ="Connely Dot Surface Generated by g_sas";
int i,i0,r0,ii0,k;
rvec *xnew;
t_atoms aaa;
if (bSave) {
i0 = atoms->nr;
r0 = atoms->nres;
srenew(atoms->atom,atoms->nr+ndots);
srenew(atoms->atomname,atoms->nr+ndots);
srenew(atoms->resinfo,r0+1);
atoms->atom[i0].resind = r0;
t_atoms_set_resinfo(atoms,i0,symtab,resnm,r0+1,' ',0,' ');
srenew(atoms->pdbinfo,atoms->nr+ndots);
snew(xnew,atoms->nr+ndots);
for(i=0; (i<atoms->nr); i++)
copy_rvec(x[i],xnew[i]);
for(i=k=0; (i<ndots); i++) {
ii0 = i0+i;
atoms->atomname[ii0] = put_symtab(symtab,atomnm);
atoms->pdbinfo[ii0].type = epdbATOM;
atoms->pdbinfo[ii0].atomnr= ii0;
atoms->atom[ii0].resind = r0;
xnew[ii0][XX] = dots[k++];
xnew[ii0][YY] = dots[k++];
xnew[ii0][ZZ] = dots[k++];
atoms->pdbinfo[ii0].bfac = 0.0;
atoms->pdbinfo[ii0].occup = 0.0;
}
atoms->nr = i0+ndots;
atoms->nres = r0+1;
write_sto_conf(fn,title,atoms,xnew,NULL,ePBC,box);
atoms->nres = r0;
atoms->nr = i0;
}
else {
init_t_atoms(&aaa,ndots,TRUE);
aaa.atom[0].resind = 0;
t_atoms_set_resinfo(&aaa,0,symtab,resnm,1,' ',0,' ');
snew(xnew,ndots);
for(i=k=0; (i<ndots); i++) {
ii0 = i;
aaa.atomname[ii0] = put_symtab(symtab,atomnm);
aaa.pdbinfo[ii0].type = epdbATOM;
aaa.pdbinfo[ii0].atomnr= ii0;
aaa.atom[ii0].resind = 0;
xnew[ii0][XX] = dots[k++];
xnew[ii0][YY] = dots[k++];
xnew[ii0][ZZ] = dots[k++];
aaa.pdbinfo[ii0].bfac = 0.0;
aaa.pdbinfo[ii0].occup = 0.0;
}
aaa.nr = ndots;
write_sto_conf(fn,title,&aaa,xnew,NULL,ePBC,box);
do_conect(fn,ndots,xnew);
free_t_atoms(&aaa,FALSE);
}
sfree(xnew);
}
int gmx_genbox(int argc, char *argv[])
{
const char *desc[] = {
"[TT]genbox[tt] can do one of 3 things:[PAR]",
"1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt]. Or specify [TT]-cs[tt] and",
"[TT]-cp[tt] with a structure file with a box, but without atoms.[PAR]",
"2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
"molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
"The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
"unless [TT]-box[tt] is set.",
"If you want the solute to be centered in the box,",
"the program [TT]editconf[tt] has sophisticated options",
"to change the box dimensions and center the solute.",
"Solvent molecules are removed from the box where the ",
"distance between any atom of the solute molecule(s) and any atom of ",
"the solvent molecule is less than the sum of the van der Waals radii of ",
"both atoms. A database ([TT]vdwradii.dat[tt]) of van der Waals radii is ",
"read by the program, and atoms not in the database are ",
"assigned a default distance [TT]-vdwd[tt].",
"Note that this option will also influence the distances between",
"solvent molecules if they contain atoms that are not in the database.",
"[PAR]",
"3) Insert a number ([TT]-nmol[tt]) of extra molecules ([TT]-ci[tt]) ",
"at random positions.",
"The program iterates until [TT]nmol[tt] molecules",
"have been inserted in the box. To test whether an insertion is ",
"successful the same van der Waals criterium is used as for removal of ",
"solvent molecules. When no appropriately-sized ",
"holes (holes that can hold an extra molecule) are available, the ",
"program tries for [TT]-nmol[tt] * [TT]-try[tt] times before giving up. ",
"Increase [TT]-try[tt] if you have several small holes to fill.[PAR]",
"If you need to do more than one of the above operations, it can be",
"best to call [TT]genbox[tt] separately for each operation, so that",
"you are sure of the order in which the operations occur.[PAR]",
"The default solvent is Simple Point Charge water (SPC), with coordinates ",
"from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
"for other 3-site water models, since a short equibilibration will remove",
"the small differences between the models.",
"Other solvents are also supported, as well as mixed solvents. The",
"only restriction to solvent types is that a solvent molecule consists",
"of exactly one residue. The residue information in the coordinate",
"files is used, and should therefore be more or less consistent.",
"In practice this means that two subsequent solvent molecules in the ",
"solvent coordinate file should have different residue number.",
"The box of solute is built by stacking the coordinates read from",
"the coordinate file. This means that these coordinates should be ",
"equlibrated in periodic boundary conditions to ensure a good",
"alignment of molecules on the stacking interfaces.",
"The [TT]-maxsol[tt] option simply adds only the first [TT]-maxsol[tt]",
"solvent molecules and leaves out the rest that would have fitted",
"into the box. This can create a void that can cause problems later.",
"Choose your volume wisely.[PAR]",
"The program can optionally rotate the solute molecule to align the",
"longest molecule axis along a box edge. This way the amount of solvent",
"molecules necessary is reduced.",
"It should be kept in mind that this only works for",
"short simulations, as e.g. an alpha-helical peptide in solution can ",
"rotate over 90 degrees, within 500 ps. In general it is therefore ",
"better to make a more or less cubic box.[PAR]",
"Setting [TT]-shell[tt] larger than zero will place a layer of water of",
"the specified thickness (nm) around the solute. Hint: it is a good",
"idea to put the protein in the center of a box first (using [TT]editconf[tt]).",
"[PAR]",
"Finally, [TT]genbox[tt] will optionally remove lines from your topology file in ",
"which a number of solvent molecules is already added, and adds a ",
"line with the total number of solvent molecules in your coordinate file."
};
const char *bugs[] = {
"Molecules must be whole in the initial configurations.",
};
/* parameter data */
gmx_bool bSol, bProt, bBox;
const char *conf_prot, *confout;
int bInsert;
real *r;
char *title_ins;
gmx_atomprop_t aps;
/* protein configuration data */
char *title = NULL;
t_atoms atoms;
rvec *x, *v = NULL;
int ePBC = -1;
matrix box;
t_pbc pbc;
/* other data types */
int atoms_added, residues_added;
t_filenm fnm[] = {
{ efSTX, "-cp", "protein", ffOPTRD },
{ efSTX, "-cs", "spc216", ffLIBOPTRD},
{ efSTX, "-ci", "insert", ffOPTRD},
{ efSTO, NULL, NULL, ffWRITE},
{ efTOP, NULL, NULL, ffOPTRW},
};
#define NFILE asize(fnm)
static int nmol_ins = 0, nmol_try = 10, seed = 1997;
static real r_distance = 0.105, r_shell = 0;
static rvec new_box = {0.0, 0.0, 0.0};
static gmx_bool bReadV = FALSE;
static int max_sol = 0;
output_env_t oenv;
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
"Box size" },
{ "-nmol", FALSE, etINT, {&nmol_ins},
"Number of extra molecules to insert" },
{ "-try", FALSE, etINT, {&nmol_try},
"Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed"},
{ "-vdwd", FALSE, etREAL, {&r_distance},
"Default van der Waals distance"},
{ "-shell", FALSE, etREAL, {&r_shell},
"Thickness of optional water layer around solute" },
{ "-maxsol", FALSE, etINT, {&max_sol},
"Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
{ "-vel", FALSE, etBOOL, {&bReadV},
"Keep velocities from input solute and solvent" }
};
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bInsert = opt2bSet("-ci", NFILE, fnm) && (nmol_ins > 0);
bSol = opt2bSet("-cs", NFILE, fnm);
bProt = opt2bSet("-cp", NFILE, fnm);
bBox = opt2parg_bSet("-box", asize(pa), pa);
/* check input */
if (bInsert && nmol_ins <= 0)
{
gmx_fatal(FARGS, "When specifying inserted molecules (-ci), "
"-nmol must be larger than 0");
}
if (!bInsert && nmol_ins > 0)
{
gmx_fatal(FARGS,
"You tried to insert molecules with -nmol, but did not supply "
"a molecule to insert with -ci.");
}
if (!bProt && !bBox)
{
gmx_fatal(FARGS, "When no solute (-cp) is specified, "
"a box size (-box) must be specified");
}
aps = gmx_atomprop_init();
if (bProt)
{
/*generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
title = read_prot(conf_prot, &atoms, &x, bReadV ? &v : NULL, &r, &ePBC, box,
aps, r_distance);
if (bReadV && !v)
{
fprintf(stderr, "Note: no velocities found\n");
}
if (atoms.nr == 0)
{
fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
bProt = FALSE;
}
}
if (!bProt)
{
atoms.nr = 0;
atoms.nres = 0;
atoms.resinfo = NULL;
atoms.atomname = NULL;
atoms.atom = NULL;
atoms.pdbinfo = NULL;
x = NULL;
r = NULL;
}
if (bBox)
{
ePBC = epbcXYZ;
clear_mat(box);
box[XX][XX] = new_box[XX];
box[YY][YY] = new_box[YY];
box[ZZ][ZZ] = new_box[ZZ];
}
if (det(box) == 0)
{
gmx_fatal(FARGS, "Undefined solute box.\nCreate one with editconf "
"or give explicit -box command line option");
}
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
if (bInsert)
{
title_ins = insert_mols(opt2fn("-ci", NFILE, fnm), nmol_ins, nmol_try, seed,
&atoms, &x, &r, ePBC, box, aps, r_distance, r_shell,
oenv);
}
else
{
title_ins = strdup("Generated by genbox");
}
/* add solvent */
if (bSol)
{
add_solv(opt2fn("-cs", NFILE, fnm), &atoms, &x, v ? &v : NULL, &r, ePBC, box,
aps, r_distance, &atoms_added, &residues_added, r_shell, max_sol,
oenv);
}
/* write new configuration 1 to file confout */
confout = ftp2fn(efSTO, NFILE, fnm);
fprintf(stderr, "Writing generated configuration to %s\n", confout);
if (bProt)
{
write_sto_conf(confout, title, &atoms, x, v, ePBC, box);
/* print box sizes and box type to stderr */
fprintf(stderr, "%s\n", title);
}
else
{
write_sto_conf(confout, title_ins, &atoms, x, v, ePBC, box);
}
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
atoms.nr, atoms.nres);
update_top(&atoms, box, NFILE, fnm, aps);
gmx_atomprop_destroy(aps);
thanx(stderr);
return 0;
}
int gmx_solvate(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] can do one of 2 things:[PAR]",
"1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt].",
"Or specify [TT]-cs[tt] and [TT]-cp[tt] with a structure file with",
"a box, but without atoms.[PAR]",
"2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
"molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
"The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
"unless [TT]-box[tt] is set.",
"If you want the solute to be centered in the box,",
"the program [gmx-editconf] has sophisticated options",
"to change the box dimensions and center the solute.",
"Solvent molecules are removed from the box where the ",
"distance between any atom of the solute molecule(s) and any atom of ",
"the solvent molecule is less than the sum of the scaled van der Waals",
"radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
"Waals radii is read by the program, and the resulting radii scaled",
"by [TT]-scale[tt]. If radii are not found in the database, those"
"atoms are assigned the (pre-scaled) distance [TT]-radius[tt].[PAR]",
"The default solvent is Simple Point Charge water (SPC), with coordinates ",
"from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
"for other 3-site water models, since a short equibilibration will remove",
"the small differences between the models.",
"Other solvents are also supported, as well as mixed solvents. The",
"only restriction to solvent types is that a solvent molecule consists",
"of exactly one residue. The residue information in the coordinate",
"files is used, and should therefore be more or less consistent.",
"In practice this means that two subsequent solvent molecules in the ",
"solvent coordinate file should have different residue number.",
"The box of solute is built by stacking the coordinates read from",
"the coordinate file. This means that these coordinates should be ",
"equlibrated in periodic boundary conditions to ensure a good",
"alignment of molecules on the stacking interfaces.",
"The [TT]-maxsol[tt] option simply adds only the first [TT]-maxsol[tt]",
"solvent molecules and leaves out the rest that would have fitted",
"into the box. This can create a void that can cause problems later.",
"Choose your volume wisely.[PAR]",
"The program can optionally rotate the solute molecule to align the",
"longest molecule axis along a box edge. This way the amount of solvent",
"molecules necessary is reduced.",
"It should be kept in mind that this only works for",
"short simulations, as e.g. an alpha-helical peptide in solution can ",
"rotate over 90 degrees, within 500 ps. In general it is therefore ",
"better to make a more or less cubic box.[PAR]",
"Setting [TT]-shell[tt] larger than zero will place a layer of water of",
"the specified thickness (nm) around the solute. Hint: it is a good",
"idea to put the protein in the center of a box first (using [gmx-editconf]).",
"[PAR]",
"Finally, [THISMODULE] will optionally remove lines from your topology file in ",
"which a number of solvent molecules is already added, and adds a ",
"line with the total number of solvent molecules in your coordinate file."
};
const char *bugs[] = {
"Molecules must be whole in the initial configurations.",
};
/* parameter data */
gmx_bool bProt, bBox;
const char *conf_prot, *confout;
real *exclusionDistances = NULL;
gmx_atomprop_t aps;
/* protein configuration data */
char *title = NULL;
t_atoms *atoms;
rvec *x = NULL, *v = NULL;
int ePBC = -1;
matrix box;
/* other data types */
int atoms_added, residues_added;
t_filenm fnm[] = {
{ efSTX, "-cp", "protein", ffOPTRD },
{ efSTX, "-cs", "spc216", ffLIBRD},
{ efSTO, NULL, NULL, ffWRITE},
{ efTOP, NULL, NULL, ffOPTRW},
};
#define NFILE asize(fnm)
static real defaultDistance = 0.105, r_shell = 0, scaleFactor = 0.57;
static rvec new_box = {0.0, 0.0, 0.0};
static gmx_bool bReadV = FALSE;
static int max_sol = 0;
output_env_t oenv;
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
"Box size (in nm)" },
{ "-radius", FALSE, etREAL, {&defaultDistance},
"Default van der Waals distance"},
{ "-scale", FALSE, etREAL, {&scaleFactor},
"Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
{ "-shell", FALSE, etREAL, {&r_shell},
"Thickness of optional water layer around solute" },
{ "-maxsol", FALSE, etINT, {&max_sol},
"Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
{ "-vel", FALSE, etBOOL, {&bReadV},
"Keep velocities from input solute and solvent" },
};
if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
const char *solventFileName = opt2fn("-cs", NFILE, fnm);
bProt = opt2bSet("-cp", NFILE, fnm);
bBox = opt2parg_bSet("-box", asize(pa), pa);
/* check input */
if (!bProt && !bBox)
{
gmx_fatal(FARGS, "When no solute (-cp) is specified, "
"a box size (-box) must be specified");
}
aps = gmx_atomprop_init();
snew(atoms, 1);
init_t_atoms(atoms, 0, FALSE);
if (bProt)
{
/* Generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
title = readConformation(conf_prot, atoms, &x,
bReadV ? &v : NULL, &ePBC, box);
exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
if (bReadV && !v)
{
fprintf(stderr, "Note: no velocities found\n");
}
if (atoms->nr == 0)
{
fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
bProt = FALSE;
}
}
if (bBox)
{
ePBC = epbcXYZ;
clear_mat(box);
box[XX][XX] = new_box[XX];
box[YY][YY] = new_box[YY];
box[ZZ][ZZ] = new_box[ZZ];
}
if (det(box) == 0)
{
gmx_fatal(FARGS, "Undefined solute box.\nCreate one with gmx editconf "
"or give explicit -box command line option");
}
add_solv(solventFileName, atoms, &x, v ? &v : NULL, &exclusionDistances, ePBC, box,
aps, defaultDistance, scaleFactor, &atoms_added, &residues_added, r_shell, max_sol,
oenv);
/* write new configuration 1 to file confout */
confout = ftp2fn(efSTO, NFILE, fnm);
fprintf(stderr, "Writing generated configuration to %s\n", confout);
if (bProt)
{
write_sto_conf(confout, title, atoms, x, v, ePBC, box);
/* print box sizes and box type to stderr */
fprintf(stderr, "%s\n", title);
}
else
{
write_sto_conf(confout, "Generated by gmx solvate", atoms, x, v, ePBC, box);
}
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
atoms->nr, atoms->nres);
update_top(atoms, box, NFILE, fnm, aps);
gmx_atomprop_destroy(aps);
sfree(exclusionDistances);
sfree(x);
sfree(v);
done_atom(atoms);
sfree(atoms);
return 0;
}
