static t_pdbfile *read_pdbf(char *fn)
{
t_pdbfile *pdbf;
double e;
char buf[256],*ptr;
int natoms;
FILE *fp;
snew(pdbf,1);
get_stx_coordnum (fn,&natoms);
init_t_atoms(&(pdbf->atoms),natoms,FALSE);
snew(pdbf->x,natoms);
read_stx_conf(fn,buf,&pdbf->atoms,pdbf->x,NULL,&pdbf->ePBC,pdbf->box);
fp = fopen(fn,"r");
do {
ptr = fgets2(buf,255,fp);
if (ptr) {
if (strstr(buf,"Intermolecular") != NULL) {
ptr = strchr(buf,'=');
sscanf(ptr+1,"%lf",&e);
pdbf->edocked = e;
}
else if (strstr(buf,"Estimated Free") != NULL) {
ptr = strchr(buf,'=');
sscanf(ptr+1,"%lf",&e);
pdbf->efree = e;
}
}
} while (ptr != NULL);
fclose(fp);
return pdbf;
}
static char *read_prot(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
real **r, int *ePBC, matrix box, gmx_atomprop_t aps,
real r_distance)
{
char *title;
int natoms;
snew(title, STRLEN);
get_stx_coordnum(confin, &natoms);
/* allocate memory for atom coordinates of configuration 1 */
snew(*x, natoms);
if (v)
{
snew(*v, natoms);
}
snew(*r, natoms);
init_t_atoms(atoms, natoms, FALSE);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr, "Reading solute configuration%s\n", v ? " and velocities" : "");
read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
title, atoms->nr, atoms->nres);
/* initialise van der waals arrays of configuration 1 */
mk_vdw(atoms, *r, aps, r_distance);
return title;
}
char *readConformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
int *ePBC, matrix box)
{
char *title;
int natoms;
snew(title, STRLEN);
get_stx_coordnum(confin, &natoms);
/* allocate memory for atom coordinates of configuration */
snew(*x, natoms);
if (v)
{
snew(*v, natoms);
}
init_t_atoms(atoms, natoms, FALSE);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr, "Reading solute configuration%s\n", v ? " and velocities" : "");
read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
title, atoms->nr, atoms->nres);
return title;
}
int read_conffile(const char *confin, char *title, rvec *x[])
{
/* read coordinates out of STX file */
int natoms;
t_atoms confat;
matrix box;
printf("read coordnumber from file %s\n", confin);
get_stx_coordnum(confin, &natoms);
printf("number of coordinates in file %d\n", natoms);
/* if (natoms != ncoords)
gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (= %d)",
confin,natoms,ncoords);
else {*/
/* make space for coordinates and velocities */
init_t_atoms(&confat, natoms, FALSE);
snew(*x, natoms);
read_stx_conf(confin, title, &confat, *x, NULL, NULL, box);
return natoms;
}
int gmx_x2top(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] generates a primitive topology from a coordinate file.",
"The program assumes all hydrogens are present when defining",
"the hybridization from the atom name and the number of bonds.",
"The program can also make an [TT].rtp[tt] entry, which you can then add",
"to the [TT].rtp[tt] database.[PAR]",
"When [TT]-param[tt] is set, equilibrium distances and angles",
"and force constants will be printed in the topology for all",
"interactions. The equilibrium distances and angles are taken",
"from the input coordinates, the force constant are set with",
"command line options.",
"The force fields somewhat supported currently are:[PAR]",
"G53a5 GROMOS96 53a5 Forcefield (official distribution)[PAR]",
"oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)[PAR]",
"The corresponding data files can be found in the library directory",
"with name [TT]atomname2type.n2t[tt]. Check Chapter 5 of the manual for more",
"information about file formats. By default, the force field selection",
"is interactive, but you can use the [TT]-ff[tt] option to specify",
"one of the short names above on the command line instead. In that",
"case [THISMODULE] just looks for the corresponding file.[PAR]",
};
const char *bugs[] = {
"The atom type selection is primitive. Virtually no chemical knowledge is used",
"Periodic boundary conditions screw up the bonding",
"No improper dihedrals are generated",
"The atoms to atomtype translation table is incomplete ([TT]atomname2type.n2t[tt] file in the data directory). Please extend it and send the results back to the GROMACS crew."
};
FILE *fp;
t_params plist[F_NRE];
t_excls *excls;
t_atoms *atoms; /* list with all atoms */
gpp_atomtype_t atype;
t_nextnb nnb;
t_nm2type *nm2t;
t_mols mymol;
int nnm;
char title[STRLEN], forcefield[32], ffdir[STRLEN];
rvec *x; /* coordinates? */
int *nbonds, *cgnr;
int bts[] = { 1, 1, 1, 2 };
matrix box; /* box length matrix */
int natoms; /* number of atoms in one molecule */
int nres; /* number of molecules? */
int i, j, k, l, m, ndih;
int epbc;
gmx_bool bRTP, bTOP, bOPLS;
t_symtab symtab;
real cutoff, qtot, mtot;
char n2t[STRLEN];
output_env_t oenv;
t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efTOP, "-o", "out", ffOPTWR },
{ efRTP, "-r", "out", ffOPTWR }
};
#define NFILE asize(fnm)
static real scale = 1.1, kb = 4e5, kt = 400, kp = 5;
static t_restp rtp_header_settings;
static gmx_bool bRemoveDihedralIfWithImproper = FALSE;
static gmx_bool bGenerateHH14Interactions = TRUE;
static gmx_bool bKeepAllGeneratedDihedrals = FALSE;
static int nrexcl = 3;
static gmx_bool bParam = TRUE, bRound = TRUE;
static gmx_bool bPairs = TRUE, bPBC = TRUE;
static gmx_bool bUsePDBcharge = FALSE, bVerbose = FALSE;
static const char *molnm = "ICE";
static const char *ff = "oplsaa";
t_pargs pa[] = {
{ "-ff", FALSE, etSTR, {&ff},
"Force field for your simulation. Type \"select\" for interactive selection." },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Generate verbose output in the top file." },
{ "-nexcl", FALSE, etINT, {&nrexcl},
"Number of exclusions" },
{ "-H14", FALSE, etBOOL, {&bGenerateHH14Interactions},
"Use 3rd neighbour interactions for hydrogen atoms" },
{ "-alldih", FALSE, etBOOL, {&bKeepAllGeneratedDihedrals},
"Generate all proper dihedrals" },
{ "-remdih", FALSE, etBOOL, {&bRemoveDihedralIfWithImproper},
"Remove dihedrals on the same bond as an improper" },
{ "-pairs", FALSE, etBOOL, {&bPairs},
"Output 1-4 interactions (pairs) in topology file" },
{ "-name", FALSE, etSTR, {&molnm},
"Name of your molecule" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions." },
{ "-pdbq", FALSE, etBOOL, {&bUsePDBcharge},
"Use the B-factor supplied in a [TT].pdb[tt] file for the atomic charges" },
{ "-param", FALSE, etBOOL, {&bParam},
"Print parameters in the output" },
{ "-round", FALSE, etBOOL, {&bRound},
"Round off measured values" },
{ "-kb", FALSE, etREAL, {&kb},
"Bonded force constant (kJ/mol/nm^2)" },
{ "-kt", FALSE, etREAL, {&kt},
"Angle force constant (kJ/mol/rad^2)" },
{ "-kp", FALSE, etREAL, {&kp},
"Dihedral angle force constant (kJ/mol/rad^2)" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
bRTP = opt2bSet("-r", NFILE, fnm);
bTOP = opt2bSet("-o", NFILE, fnm);
/* C89 requirements mean that these struct members cannot be used in
* the declaration of pa. So some temporary variables are needed. */
rtp_header_settings.bRemoveDihedralIfWithImproper = bRemoveDihedralIfWithImproper;
rtp_header_settings.bGenerateHH14Interactions = bGenerateHH14Interactions;
rtp_header_settings.bKeepAllGeneratedDihedrals = bKeepAllGeneratedDihedrals;
rtp_header_settings.nrexcl = nrexcl;
if (!bRTP && !bTOP)
{
gmx_fatal(FARGS, "Specify at least one output file");
}
/* Force field selection, interactive or direct */
choose_ff(strcmp(ff, "select") == 0 ? NULL : ff,
forcefield, sizeof(forcefield),
ffdir, sizeof(ffdir));
bOPLS = (strcmp(forcefield, "oplsaa") == 0);
mymol.name = strdup(molnm);
mymol.nr = 1;
/* Init parameter lists */
init_plist(plist);
/* Read coordinates */
get_stx_coordnum(opt2fn("-f", NFILE, fnm), &natoms);
snew(atoms, 1);
/* make space for all the atoms */
init_t_atoms(atoms, natoms, TRUE);
snew(x, natoms);
read_stx_conf(opt2fn("-f", NFILE, fnm), title, atoms, x, NULL, &epbc, box);
sprintf(n2t, "%s", ffdir);
nm2t = rd_nm2type(n2t, &nnm);
if (nnm == 0)
{
gmx_fatal(FARGS, "No or incorrect atomname2type.n2t file found (looking for %s)",
n2t);
}
else
{
printf("There are %d name to type translations in file %s\n", nnm, n2t);
}
if (debug)
{
dump_nm2type(debug, nnm, nm2t);
}
printf("Generating bonds from distances...\n");
snew(nbonds, atoms->nr);
mk_bonds(nnm, nm2t, atoms, x, &(plist[F_BONDS]), nbonds, bPBC, box);
open_symtab(&symtab);
atype = set_atom_type(&symtab, atoms, &(plist[F_BONDS]), nbonds, nnm, nm2t);
/* Make Angles and Dihedrals */
snew(excls, atoms->nr);
printf("Generating angles and dihedrals from bonds...\n");
init_nnb(&nnb, atoms->nr, 4);
gen_nnb(&nnb, plist);
print_nnb(&nnb, "NNB");
gen_pad(&nnb, atoms, &rtp_header_settings, plist, excls, NULL, TRUE);
done_nnb(&nnb);
if (!bPairs)
{
plist[F_LJ14].nr = 0;
}
fprintf(stderr,
"There are %4d %s dihedrals, %4d impropers, %4d angles\n"
" %4d pairs, %4d bonds and %4d atoms\n",
plist[F_PDIHS].nr,
bOPLS ? "Ryckaert-Bellemans" : "proper",
plist[F_IDIHS].nr, plist[F_ANGLES].nr,
plist[F_LJ14].nr, plist[F_BONDS].nr, atoms->nr);
calc_angles_dihs(&plist[F_ANGLES], &plist[F_PDIHS], x, bPBC, box);
set_force_const(plist, kb, kt, kp, bRound, bParam);
cgnr = set_cgnr(atoms, bUsePDBcharge, &qtot, &mtot);
printf("Total charge is %g, total mass is %g\n", qtot, mtot);
if (bOPLS)
{
bts[2] = 3;
bts[3] = 1;
}
if (bTOP)
{
fp = ftp2FILE(efTOP, NFILE, fnm, "w");
print_top_header(fp, ftp2fn(efTOP, NFILE, fnm), TRUE, ffdir, 1.0);
write_top(fp, NULL, mymol.name, atoms, FALSE, bts, plist, excls, atype,
cgnr, rtp_header_settings.nrexcl);
print_top_mols(fp, mymol.name, ffdir, NULL, 0, NULL, 1, &mymol);
ffclose(fp);
}
if (bRTP)
{
print_rtp(ftp2fn(efRTP, NFILE, fnm), "Generated by x2top",
atoms, plist, atype, cgnr);
}
if (debug)
{
dump_hybridization(debug, atoms, nbonds);
}
close_symtab(&symtab);
free(mymol.name);
printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",
ShortProgram());
printf(" Please verify atomtypes and charges by comparison to other\n");
printf(" topologies.\n");
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;
}
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_dyndom(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_dyndom[tt] reads a [TT].pdb[tt] file output from DynDom",
"(http://www.cmp.uea.ac.uk/dyndom/).",
"It reads the coordinates, the coordinates of the rotation axis,",
"and an index file containing the domains.",
"Furthermore, it takes the first and last atom of the arrow file",
"as command line arguments (head and tail) and",
"finally it takes the translation vector (given in DynDom info file)",
"and the angle of rotation (also as command line arguments). If the angle",
"determined by DynDom is given, one should be able to recover the",
"second structure used for generating the DynDom output.",
"Because of limited numerical accuracy this should be verified by",
"computing an all-atom RMSD (using [TT]g_confrms[tt]) rather than by file",
"comparison (using diff).[PAR]",
"The purpose of this program is to interpolate and extrapolate the",
"rotation as found by DynDom. As a result unphysical structures with",
"long or short bonds, or overlapping atoms may be produced. Visual",
"inspection, and energy minimization may be necessary to",
"validate the structure."
};
static real trans0 = 0;
static rvec head = { 0, 0, 0 };
static rvec tail = { 0, 0, 0 };
static real angle0 = 0, angle1 = 0, maxangle = 0;
static int label = 0, nframes = 11;
t_pargs pa[] = {
{ "-firstangle", FALSE, etREAL, {&angle0},
"Angle of rotation about rotation vector" },
{ "-lastangle", FALSE, etREAL, {&angle1},
"Angle of rotation about rotation vector" },
{ "-nframe", FALSE, etINT, {&nframes},
"Number of steps on the pathway" },
{ "-maxangle", FALSE, etREAL, {&maxangle},
"DymDom dtermined angle of rotation about rotation vector" },
{ "-trans", FALSE, etREAL, {&trans0},
"Translation (Angstrom) along rotation vector (see DynDom info file)" },
{ "-head", FALSE, etRVEC, {head},
"First atom of the arrow vector" },
{ "-tail", FALSE, etRVEC, {tail},
"Last atom of the arrow vector" }
};
int i, j, natoms, isize;
t_trxstatus *status;
atom_id *index = NULL, *index_all;
char title[256], *grpname;
t_atoms atoms;
real angle, trans;
rvec *x, *v, *xout, *vout;
matrix box;
output_env_t oenv;
t_filenm fnm[] = {
{ efPDB, "-f", "dyndom", ffREAD },
{ efTRO, "-o", "rotated", ffWRITE },
{ efNDX, "-n", "domains", ffREAD }
};
#define NFILE asize(fnm)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv);
get_stx_coordnum (opt2fn("-f", NFILE, fnm), &natoms);
init_t_atoms(&atoms, natoms, TRUE);
snew(x, natoms);
snew(v, natoms);
read_stx_conf(opt2fn("-f", NFILE, fnm), title, &atoms, x, v, NULL, box);
snew(xout, natoms);
snew(vout, natoms);
printf("Select group to rotate:\n");
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
printf("Going to rotate %s containg %d atoms\n", grpname, isize);
snew(index_all, atoms.nr);
for (i = 0; (i < atoms.nr); i++)
{
index_all[i] = i;
}
status = open_trx(opt2fn("-o", NFILE, fnm), "w");
label = 'A';
for (i = 0; (i < nframes); i++, label++)
{
angle = angle0 + (i*(angle1-angle0))/(nframes-1);
trans = trans0*0.1*angle/maxangle;
printf("Frame: %2d (label %c), angle: %8.3f deg., trans: %8.3f nm\n",
i, label, angle, trans);
rot_conf(&atoms, x, v, trans, angle, head, tail, box, isize, index, xout, vout);
if (label > 'Z')
{
label -= 26;
}
for (j = 0; (j < atoms.nr); j++)
{
atoms.resinfo[atoms.atom[j].resind].chainid = label;
}
write_trx(status, atoms.nr, index_all, &atoms, i, angle, box, xout, vout, NULL);
}
close_trx(status);
thanx(stderr);
return 0;
}
int main(int argc, char *argv[])
{
t_symtab tab;
static char *desc[] = {
"[TT]hexamer[tt] takes a single input coordinate file and makes five symmetry",
"related copies."
};
#define NPA asize(pa)
t_filenm fnm[] = {
{ efSTX, "-f", NULL, ffREAD },
{ efPDB, "-o", NULL, ffWRITE }
};
#define NFILE asize(fnm)
gmx_bool bCenter = FALSE;
gmx_bool bTrimer = FALSE;
gmx_bool bAlternate = FALSE;
real rDist = 0,rAngleZ = 0,rAngleX = 0, alterz = 0;
t_pargs pa[] = {
{ "-center", FALSE, etBOOL, {&bCenter},
"Center molecule on Z-axis first" },
{ "-trimer", FALSE, etBOOL, {&bTrimer},
"Make trimer rather than hexamer" },
{ "-alternate",FALSE, etBOOL, {&bAlternate},
"Turn every other molecule upside down" },
{ "-alterz", FALSE, etREAL, {&alterz},
"Add this amount to Z-coordinate in every other molecule" },
{ "-radius", FALSE, etREAL, {&rDist},
"Distance of protein axis from Z-axis (implies [TT]-center[tt])" },
{ "-anglez", FALSE, etREAL, {&rAngleZ},
"Initial angle of rotation around Z-axis of protein" },
{ "-anglex", FALSE, etREAL, {&rAngleX},
"Initial angle of rotation around X-axis of protein" }
};
#define NPA asize(pa)
FILE *fp;
int i,iout,now,natom;
rvec *xin,*vin,*xout;
matrix box;
t_atoms atoms,aout;
char *infile,*outfile,title[256],buf[32];
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,
asize(desc),desc,0,NULL);
bCenter = bCenter || (rDist > 0) || bAlternate;
infile = ftp2fn(efSTX,NFILE,fnm);
outfile = ftp2fn(efPDB,NFILE,fnm);
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(xin,natom);
snew(xout,natom);
snew(vin,natom);
read_stx_conf(infile,title,&atoms,xin,vin,box);
printf("Read %d atoms\n",atoms.nr);
if (bCenter)
prep_x(atoms.nr,xin,rDist,rAngleZ,rAngleX);
fp = gmx_ffopen(outfile,"w");
for(i=0; (i<(bTrimer ? 3 : 6)); i++) {
rotate_x(atoms.nr,xin,i*(bTrimer ? 120.0 : 60.0),xout,TRUE,
bAlternate && ((i % 2) != 0),alterz*(((i % 2) == 0) ? 0 : 1));
sprintf(buf,"Rotated %d degrees",i*(bTrimer ? 120 : 60));
write_pdbfile(fp,buf,&atoms,xout,box,'A'+i,1+i);
}
gmx_ffclose(fp);
gmx_thanx(stderr);
return 0;
}
static void read_posres(gmx_mtop_t *mtop,t_molinfo *molinfo,bool bTopB,
char *fn,
int rc_scaling, int ePBC,
rvec com)
{
bool bFirst = TRUE;
rvec *x,*v,*xp;
dvec sum;
double totmass;
t_atoms dumat;
matrix box,invbox;
int natoms,npbcdim=0;
char title[STRLEN];
int a,i,ai,j,k,mb,nat_molb;
gmx_molblock_t *molb;
t_params *pr;
t_atom *atom;
get_stx_coordnum(fn,&natoms);
if (natoms != mtop->natoms) {
sprintf(warn_buf,"The number of atoms in %s (%d) does not match the number of atoms in the topology (%d). Will assume that the first %d atoms in the topology and %s match.",fn,natoms,mtop->natoms,min(mtop->natoms,natoms),fn);
warning(NULL);
}
snew(x,natoms);
snew(v,natoms);
init_t_atoms(&dumat,natoms,FALSE);
read_stx_conf(fn,title,&dumat,x,v,NULL,box);
npbcdim = ePBC2npbcdim(ePBC);
clear_rvec(com);
if (rc_scaling != erscNO) {
copy_mat(box,invbox);
for(j=npbcdim; j<DIM; j++) {
clear_rvec(invbox[j]);
invbox[j][j] = 1;
}
m_inv_ur0(invbox,invbox);
}
/* Copy the reference coordinates to mtop */
clear_dvec(sum);
totmass = 0;
a = 0;
for(mb=0; mb<mtop->nmolblock; mb++) {
molb = &mtop->molblock[mb];
nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
pr = &(molinfo[molb->type].plist[F_POSRES]);
if (pr->nr > 0) {
atom = mtop->moltype[molb->type].atoms.atom;
for(i=0; (i<pr->nr); i++) {
ai=pr->param[i].AI;
if (ai >= natoms) {
gmx_fatal(FARGS,"Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
ai+1,*molinfo[molb->type].name,fn,natoms);
}
if (rc_scaling == erscCOM) {
/* Determine the center of mass of the posres reference coordinates */
for(j=0; j<npbcdim; j++) {
sum[j] += atom[ai].m*x[a+ai][j];
}
totmass += atom[ai].m;
}
}
if (!bTopB) {
molb->nposres_xA = nat_molb;
snew(molb->posres_xA,molb->nposres_xA);
for(i=0; i<nat_molb; i++) {
copy_rvec(x[a+i],molb->posres_xA[i]);
}
} else {
molb->nposres_xB = nat_molb;
snew(molb->posres_xB,molb->nposres_xB);
for(i=0; i<nat_molb; i++) {
copy_rvec(x[a+i],molb->posres_xB[i]);
}
}
}
a += nat_molb;
}
if (rc_scaling == erscCOM) {
if (totmass == 0)
gmx_fatal(FARGS,"The total mass of the position restraint atoms is 0");
for(j=0; j<npbcdim; j++)
com[j] = sum[j]/totmass;
fprintf(stderr,"The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n",com[XX],com[YY],com[ZZ]);
}
if (rc_scaling != erscNO) {
for(mb=0; mb<mtop->nmolblock; mb++) {
molb = &mtop->molblock[mb];
nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
if (molb->nposres_xA > 0 || molb->nposres_xB > 0) {
xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
for(i=0; i<nat_molb; i++) {
for(j=0; j<npbcdim; j++) {
if (rc_scaling == erscALL) {
/* Convert from Cartesian to crystal coordinates */
xp[i][j] *= invbox[j][j];
for(k=j+1; k<npbcdim; k++) {
xp[i][j] += invbox[k][j]*xp[i][k];
}
} else if (rc_scaling == erscCOM) {
/* Subtract the center of mass */
xp[i][j] -= com[j];
}
}
}
}
}
if (rc_scaling == erscCOM) {
/* Convert the COM from Cartesian to crystal coordinates */
for(j=0; j<npbcdim; j++) {
com[j] *= invbox[j][j];
for(k=j+1; k<npbcdim; k++) {
com[j] += invbox[k][j]*com[k];
}
}
}
}
free_t_atoms(&dumat,TRUE);
sfree(x);
sfree(v);
}
gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
rvec **x, rvec **v, matrix box, gmx_bool bMass)
{
t_tpxheader header;
int natoms, i;
gmx_bool bTop, bXNULL = FALSE;
gmx_mtop_t *mtop;
gmx_atomprop_t aps;
bTop = fn2bTPX(infile);
if (ePBC != NULL)
{
*ePBC = -1;
}
if (bTop)
{
read_tpxheader(infile, &header, TRUE);
if (x)
{
snew(*x, header.natoms);
}
if (v)
{
snew(*v, header.natoms);
}
snew(mtop, 1);
int ePBC_tmp
= read_tpx(infile, NULL, box, &natoms,
(x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, mtop);
if (ePBC != NULL)
{
*ePBC = ePBC_tmp;
}
*top = gmx_mtop_t_to_t_topology(mtop);
/* In this case we need to throw away the group data too */
done_gmx_groups_t(&mtop->groups);
sfree(mtop);
tpx_make_chain_identifiers(&top->atoms, &top->mols);
}
else
{
open_symtab(&top->symtab);
get_stx_coordnum(infile, &natoms);
init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
if (x == NULL)
{
snew(x, 1);
bXNULL = TRUE;
}
snew(*x, natoms);
if (v)
{
snew(*v, natoms);
}
read_stx_conf(infile, top, *x, (v == NULL) ? NULL : *v, ePBC, box);
if (bXNULL)
{
sfree(*x);
sfree(x);
}
if (bMass)
{
aps = gmx_atomprop_init();
for (i = 0; (i < natoms); i++)
{
if (!gmx_atomprop_query(aps, epropMass,
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i],
&(top->atoms.atom[i].m)))
{
if (debug)
{
fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
top->atoms.resinfo[top->atoms.atom[i].resind].nr,
*top->atoms.atomname[i]);
}
}
}
gmx_atomprop_destroy(aps);
}
top->idef.ntypes = -1;
}
return bTop;
}
static char *insert_mols(char *mol_insrt,int nmol_insrt,int ntry,int seed,
t_atoms *atoms,rvec **x,real **r,int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,real rshell)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt,*x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i,mol,onr;
real alfa,beta,gamma;
rvec offset_x;
int try;
set_pbc(&pbc,ePBC,box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt,&atoms_insrt.nr);
if (atoms_insrt.nr == 0)
gmx_fatal(FARGS,"No molecule in %s, please check your input\n",mol_insrt);
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt,atoms_insrt.nr);
snew(r_insrt,atoms_insrt.nr);
snew(atoms_insrt.resname,atoms_insrt.nr);
snew(atoms_insrt.atomname,atoms_insrt.nr);
snew(atoms_insrt.atom,atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n,atoms_insrt.nr);
snew(title_insrt,STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr,"Reading molecule configuration \n");
read_stx_conf(mol_insrt,title_insrt,&atoms_insrt,x_insrt,NULL,
&ePBC_insrt,box_insrt);
fprintf(stderr,"%s\nContaining %d atoms in %d residue\n",
title_insrt,atoms_insrt.nr,atoms_insrt.nres);
srenew(atoms_insrt.resname,atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt,r_insrt,aps,r_distance);
srenew(atoms->resname,(atoms->nres+nmol_insrt));
srenew(atoms->atomname,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r,(atoms->nr+atoms_insrt.nr*nmol_insrt));
try=mol=0;
while ((mol < nmol_insrt) && (try < ntry*nmol_insrt)) {
fprintf(stderr,"\rTry %d",try++);
for (i=0;(i<atoms_insrt.nr);i++) {
if (atoms_insrt.atom[i].resnr!=0)
gmx_fatal(FARGS,"more then one residue in insert molecules\n"
"program terminated\n");
copy_rvec(x_insrt[i],x_n[i]);
}
alfa=2*M_PI*rando(&seed);
beta=2*M_PI*rando(&seed);
gamma=2*M_PI*rando(&seed);
rotate_conf(atoms_insrt.nr,x_n,NULL,alfa,beta,gamma);
offset_x[XX]=box[XX][XX]*rando(&seed);
offset_x[YY]=box[YY][YY]*rando(&seed);
offset_x[ZZ]=box[ZZ][ZZ]*rando(&seed);
gen_box(0,atoms_insrt.nr,x_n,box_insrt,offset_x,TRUE);
if (!in_box(&pbc,x_n[0]) || !in_box(&pbc,x_n[atoms_insrt.nr-1]))
continue;
onr=atoms->nr;
add_conf(atoms,x,NULL,r,FALSE,ePBC,box,TRUE,
&atoms_insrt,x_n,NULL,r_insrt,FALSE,rshell,0);
if (atoms->nr==(atoms_insrt.nr+onr)) {
mol++;
fprintf(stderr," success (now %d atoms)!",atoms->nr);
}
}
srenew(atoms->resname, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr,"\n");
/* print number of molecules added */
fprintf(stderr,"Added %d molecules (out of %d requested) of %s\n",
mol,nmol_insrt,*atoms_insrt.resname[0]);
return title_insrt;
}
static void add_solv(char *fn,t_atoms *atoms,rvec **x,rvec **v,real **r,
int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,int *atoms_added,
int *residues_added,real rshell,int max_sol)
{
int i,nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt,*v_solvt=NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr,onres;
strncpy(filename,libfn(fn),STRLEN);
snew(atoms_solvt,1);
get_stx_coordnum(filename,&(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
gmx_fatal(FARGS,"No solvent in %s, please check your input\n",filename);
snew(x_solvt,atoms_solvt->nr);
if (v) snew(v_solvt,atoms_solvt->nr);
snew(r_solvt,atoms_solvt->nr);
snew(atoms_solvt->resname,atoms_solvt->nr);
snew(atoms_solvt->atomname,atoms_solvt->nr);
snew(atoms_solvt->atom,atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr,"Reading solvent configuration%s\n",
v_solvt?" and velocities":"");
read_stx_conf(filename,title_solvt,atoms_solvt,x_solvt,v_solvt,
&ePBC_solvt,box_solvt);
fprintf(stderr,"\"%s\"\n",title_solvt);
fprintf(stderr,"solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr,atoms_solvt->nres);
fprintf(stderr,"\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt,x_solvt,box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt,r_solvt,aps,r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol=1;
for (i=0; (i < DIM);i++) {
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
n_box[i]++;
nmol*=n_box[i];
}
fprintf(stderr,"Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX],n_box[YY],n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resname,atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname,atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom,atoms_solvt->nr*nmol);
srenew(x_solvt,atoms_solvt->nr*nmol);
if (v_solvt) srenew(v_solvt,atoms_solvt->nr*nmol);
srenew(r_solvt,atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt,x_solvt,v_solvt,r_solvt,box_solvt,n_box);
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt,x_solvt,v_solvt,r_solvt);
/* add the two configurations */
onr=atoms->nr;
onres=atoms->nres;
add_conf(atoms,x,v,r,TRUE,ePBC,box,FALSE,
atoms_solvt,x_solvt,v_solvt,r_solvt,TRUE,rshell,max_sol);
*atoms_added=atoms->nr-onr;
*residues_added=atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr,"Generated solvent containing %d atoms in %d residues\n",
*atoms_added,*residues_added);
}
int gmx_morph(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] does a linear interpolation of conformations in order to",
"create intermediates. Of course these are completely unphysical, but",
"that you may try to justify yourself. Output is in the form of a ",
"generic trajectory. The number of intermediates can be controlled with",
"the [TT]-ninterm[tt] flag. The first and last flag correspond to the way of",
"interpolating: 0 corresponds to input structure 1 while",
"1 corresponds to input structure 2.",
"If you specify [TT]-first[tt] < 0 or [TT]-last[tt] > 1 extrapolation will be",
"on the path from input structure x[SUB]1[sub] to x[SUB]2[sub]. In general, the coordinates",
"of the intermediate x(i) out of N total intermediates correspond to:[PAR]",
"x(i) = x[SUB]1[sub] + (first+(i/(N-1))*(last-first))*(x[SUB]2[sub]-x[SUB]1[sub])[PAR]",
"Finally the RMSD with respect to both input structures can be computed",
"if explicitly selected ([TT]-or[tt] option). In that case, an index file may be",
"read to select the group from which the RMS is computed."
};
t_filenm fnm[] = {
{ efSTX, "-f1", "conf1", ffREAD },
{ efSTX, "-f2", "conf2", ffREAD },
{ efTRX, "-o", "interm", ffWRITE },
{ efXVG, "-or", "rms-interm", ffOPTWR },
{ efNDX, "-n", "index", ffOPTRD }
};
#define NFILE asize(fnm)
static int ninterm = 11;
static real first = 0.0;
static real last = 1.0;
static gmx_bool bFit = TRUE;
t_pargs pa [] = {
{ "-ninterm", FALSE, etINT, {&ninterm},
"Number of intermediates" },
{ "-first", FALSE, etREAL, {&first},
"Corresponds to first generated structure (0 is input x[SUB]1[sub], see above)" },
{ "-last", FALSE, etREAL, {&last},
"Corresponds to last generated structure (1 is input x[SUB]2[sub], see above)" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Do a least squares fit of the second to the first structure before interpolating" }
};
const char *leg[] = { "Ref = 1\\Sst\\N conf", "Ref = 2\\Snd\\N conf" };
FILE *fp = NULL;
int i, isize, is_lsq, nat1, nat2;
t_trxstatus *status;
atom_id *index, *index_lsq, *index_all, *dummy;
t_atoms atoms;
rvec *x1, *x2, *xx, *v;
matrix box;
real rms1, rms2, fac, *mass;
char title[STRLEN], *grpname;
gmx_bool bRMS;
output_env_t oenv;
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc,
0, NULL, &oenv))
{
return 0;
}
get_stx_coordnum (opt2fn("-f1", NFILE, fnm), &nat1);
get_stx_coordnum (opt2fn("-f2", NFILE, fnm), &nat2);
if (nat1 != nat2)
{
gmx_fatal(FARGS, "Number of atoms in first structure is %d, in second %d",
nat1, nat2);
}
init_t_atoms(&atoms, nat1, TRUE);
snew(x1, nat1);
snew(x2, nat1);
snew(xx, nat1);
snew(v, nat1);
read_stx_conf(opt2fn("-f1", NFILE, fnm), title, &atoms, x1, v, NULL, box);
read_stx_conf(opt2fn("-f2", NFILE, fnm), title, &atoms, x2, v, NULL, box);
snew(mass, nat1);
snew(index_all, nat1);
for (i = 0; (i < nat1); i++)
{
mass[i] = 1;
index_all[i] = i;
}
if (bFit)
{
printf("Select group for LSQ superposition:\n");
get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &is_lsq, &index_lsq,
&grpname);
reset_x(is_lsq, index_lsq, nat1, index_all, x1, mass);
reset_x(is_lsq, index_lsq, nat1, index_all, x2, mass);
do_fit(nat1, mass, x1, x2);
}
bRMS = opt2bSet("-or", NFILE, fnm);
if (bRMS)
{
fp = xvgropen(opt2fn("-or", NFILE, fnm), "RMSD", "Conf", "(nm)", oenv);
xvgr_legend(fp, asize(leg), leg, oenv);
printf("Select group for RMSD calculation:\n");
get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &isize, &index, &grpname);
printf("You selected group %s, containing %d atoms\n", grpname, isize);
rms1 = rmsdev_ind(isize, index, mass, x1, x2);
fprintf(stderr, "RMSD between input conformations is %g nm\n", rms1);
}
snew(dummy, nat1);
for (i = 0; (i < nat1); i++)
{
dummy[i] = i;
}
status = open_trx(ftp2fn(efTRX, NFILE, fnm), "w");
for (i = 0; (i < ninterm); i++)
{
fac = dointerp(nat1, x1, x2, xx, i, ninterm, first, last);
write_trx(status, nat1, dummy, &atoms, i, fac, box, xx, NULL, NULL);
if (bRMS)
{
rms1 = rmsdev_ind(isize, index, mass, x1, xx);
rms2 = rmsdev_ind(isize, index, mass, x2, xx);
fprintf(fp, "%10g %10g %10g\n", fac, rms1, rms2);
}
}
close_trx(status);
if (bRMS)
{
gmx_ffclose(fp);
do_view(oenv, opt2fn("-or", NFILE, fnm), "-nxy");
}
return 0;
}
int gmx_genpr(int argc,char *argv[])
{
const char *desc[] = {
"[TT]genrestr[tt] produces an include file for a topology containing",
"a list of atom numbers and three force constants for the",
"[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction. A single isotropic force constant may",
"be given on the command line instead of three components.[PAR]",
"WARNING: position restraints only work for the one molecule at a time.",
"Position restraints are interactions within molecules, therefore",
"they should be included within the correct [TT][ moleculetype ][tt]",
"block in the topology. Since the atom numbers in every moleculetype",
"in the topology start at 1 and the numbers in the input file for",
"[TT]genrestr[tt] number consecutively from 1, [TT]genrestr[tt] will only",
"produce a useful file for the first molecule.[PAR]",
"The [TT]-of[tt] option produces an index file that can be used for",
"freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
"With the [TT]-disre[tt] option, half a matrix of distance restraints",
"is generated instead of position restraints. With this matrix, that",
"one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can",
"maintain the overall conformation of a protein without tieing it to",
"a specific position (as with position restraints)."
};
static rvec fc={1000.0,1000.0,1000.0};
static real freeze_level = 0.0;
static real disre_dist = 0.1;
static real disre_frac = 0.0;
static real disre_up2 = 1.0;
static gmx_bool bDisre=FALSE;
static gmx_bool bConstr=FALSE;
static real cutoff = -1.0;
t_pargs pa[] = {
{ "-fc", FALSE, etRVEC, {fc},
"force constants (kJ/mol nm^2)" },
{ "-freeze", FALSE, etREAL, {&freeze_level},
"if the [TT]-of[tt] option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here" },
{ "-disre", FALSE, etBOOL, {&bDisre},
"Generate a distance restraint matrix for all the atoms in index" },
{ "-disre_dist", FALSE, etREAL, {&disre_dist},
"Distance range around the actual distance for generating distance restraints" },
{ "-disre_frac", FALSE, etREAL, {&disre_frac},
"Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead." },
{ "-disre_up2", FALSE, etREAL, {&disre_up2},
"Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)" },
{ "-cutoff", FALSE, etREAL, {&cutoff},
"Only generate distance restraints for atoms pairs within cutoff (nm)" },
{ "-constr", FALSE, etBOOL, {&bConstr},
"Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions." }
};
#define npargs asize(pa)
output_env_t oenv;
t_atoms *atoms=NULL;
int i,j,k;
FILE *out;
int igrp;
real d,dd,lo,hi;
atom_id *ind_grp;
const char *xfn,*nfn;
char *gn_grp;
char title[STRLEN];
matrix box;
gmx_bool bFreeze;
rvec dx,*x=NULL,*v=NULL;
t_filenm fnm[] = {
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efITP, "-o", "posre", ffWRITE },
{ efNDX, "-of", "freeze", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,npargs,pa,
asize(desc),desc,0,NULL,&oenv);
bFreeze = opt2bSet("-of",NFILE,fnm) || opt2parg_bSet("-freeze",asize(pa),pa);
bDisre = bDisre || opt2parg_bSet("-disre_dist",npargs,pa);
xfn = opt2fn_null("-f",NFILE,fnm);
nfn = opt2fn_null("-n",NFILE,fnm);
if (( nfn == NULL ) && ( xfn == NULL))
gmx_fatal(FARGS,"no index file and no structure file suplied");
if ((disre_frac < 0) || (disre_frac >= 1))
gmx_fatal(FARGS,"disre_frac should be between 0 and 1");
if (disre_dist < 0)
gmx_fatal(FARGS,"disre_dist should be >= 0");
if (xfn != NULL) {
snew(atoms,1);
get_stx_coordnum(xfn,&(atoms->nr));
init_t_atoms(atoms,atoms->nr,TRUE);
snew(x,atoms->nr);
snew(v,atoms->nr);
fprintf(stderr,"\nReading structure file\n");
read_stx_conf(xfn,title,atoms,x,v,NULL,box);
}
if (bFreeze) {
if (atoms && atoms->pdbinfo)
gmx_fatal(FARGS,"No B-factors in input file %s, use a pdb file next time.",
xfn);
out=opt2FILE("-of",NFILE,fnm,"w");
fprintf(out,"[ freeze ]\n");
for(i=0; (i<atoms->nr); i++) {
if (atoms->pdbinfo[i].bfac <= freeze_level)
fprintf(out,"%d\n",i+1);
}
ffclose(out);
}
else if ((bDisre || bConstr) && x) {
printf("Select group to generate %s matrix from\n",
bConstr ? "constraint" : "distance restraint");
get_index(atoms,nfn,1,&igrp,&ind_grp,&gn_grp);
out=ftp2FILE(efITP,NFILE,fnm,"w");
if (bConstr) {
fprintf(out,"; constraints for %s of %s\n\n",gn_grp,title);
fprintf(out,"[ constraints ]\n");
fprintf(out,";%4s %5s %1s %10s\n","i","j","tp","dist");
}
else {
fprintf(out,"; distance restraints for %s of %s\n\n",gn_grp,title);
fprintf(out,"[ distance_restraints ]\n");
fprintf(out,";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n","i","j","?",
"label","funct","lo","up1","up2","weight");
}
for(i=k=0; i<igrp; i++)
for(j=i+1; j<igrp; j++,k++) {
rvec_sub(x[ind_grp[i]],x[ind_grp[j]],dx);
d = norm(dx);
if (bConstr)
fprintf(out,"%5d %5d %1d %10g\n",ind_grp[i]+1,ind_grp[j]+1,2,d);
else {
if (cutoff < 0 || d < cutoff)
{
if (disre_frac > 0)
dd = min(disre_dist,disre_frac*d);
else
dd = disre_dist;
lo = max(0,d-dd);
hi = d+dd;
fprintf(out,"%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
ind_grp[i]+1,ind_grp[j]+1,1,k,1,
lo,hi,hi+1,1.0);
}
}
}
ffclose(out);
}
else {
printf("Select group to position restrain\n");
get_index(atoms,nfn,1,&igrp,&ind_grp,&gn_grp);
out=ftp2FILE(efITP,NFILE,fnm,"w");
fprintf(out,"; position restraints for %s of %s\n\n",gn_grp,title);
fprintf(out,"[ position_restraints ]\n");
fprintf(out,";%3s %5s %9s %10s %10s\n","i","funct","fcx","fcy","fcz");
for(i=0; i<igrp; i++)
fprintf(out,"%4d %4d %10g %10g %10g\n",
ind_grp[i]+1,1,fc[XX],fc[YY],fc[ZZ]);
ffclose(out);
}
if (xfn) {
sfree(x);
sfree(v);
}
thanx(stderr);
return 0;
}
int gmx_chi(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_chi[tt] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your ",
"amino acid backbone and sidechains.",
"It can compute dihedral angle as a function of time, and as",
"histogram distributions.",
"The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
"If option [TT]-corr[tt] is given, the program will",
"calculate dihedral autocorrelation functions. The function used",
"is C(t) = < cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+t)) >. The use of cosines",
"rather than angles themselves, resolves the problem of periodicity.",
"(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
"Separate files for each dihedral of each residue",
"[TT](corr(dihedral)(RESIDUE)(nresnr).xvg[tt]) are output, as well as a",
"file containing the information for all residues (argument of [TT]-corr[tt]).[PAR]",
"With option [TT]-all[tt], the angles themselves as a function of time for",
"each residue are printed to separate files [TT](dihedral)(RESIDUE)(nresnr).xvg[tt].",
"These can be in radians or degrees.[PAR]",
"A log file (argument [TT]-g[tt]) is also written. This contains [BR]",
"(a) information about the number of residues of each type.[BR]",
"(b) The NMR ^3J coupling constants from the Karplus equation.[BR]",
"(c) a table for each residue of the number of transitions between ",
"rotamers per nanosecond, and the order parameter S^2 of each dihedral.[BR]",
"(d) a table for each residue of the rotamer occupancy.[PAR]",
"All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
"to planar groups (i.e. [GRK]chi[grk]2 of aromatics, Asp and Asn; [GRK]chi[grk]3 of Glu",
"and Gln; and [GRK]chi[grk]4 of Arg), which are 2-fold. \"rotamer 0\" means ",
"that the dihedral was not in the core region of each rotamer. ",
"The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
"The S^2 order parameters are also output to an [TT].xvg[tt] file",
"(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
"the S^2 values as B-factor (argument [TT]-p[tt]). ",
"The total number of rotamer transitions per timestep",
"(argument [TT]-ot[tt]), the number of transitions per rotamer",
"(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
"can also be written to [TT].xvg[tt] files.[PAR]",
"If [TT]-chi_prod[tt] is set (and [TT]-maxchi[tt] > 0), cumulative rotamers, e.g.",
"1+9([GRK]chi[grk]1-1)+3([GRK]chi[grk]2-1)+([GRK]chi[grk]3-1) (if the residue has three 3-fold ",
"dihedrals and [TT]-maxchi[tt] >= 3)",
"are calculated. As before, if any dihedral is not in the core region,",
"the rotamer is taken to be 0. The occupancies of these cumulative ",
"rotamers (starting with rotamer 0) are written to the file",
"that is the argument of [TT]-cp[tt], and if the [TT]-all[tt] flag",
"is given, the rotamers as functions of time",
"are written to [TT]chiproduct(RESIDUE)(nresnr).xvg[tt] ",
"and their occupancies to [TT]histo-chiproduct(RESIDUE)(nresnr).xvg[tt].[PAR]",
"The option [TT]-r[tt] generates a contour plot of the average [GRK]omega[grk] angle",
"as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot",
"the average [GRK]omega[grk] angle is plotted using color coding.",
};
const char *bugs[] = {
"Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.",
"[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like [TT]g_rama[tt].",
"[TT]-r0[tt] option does not work properly",
"Rotamers with multiplicity 2 are printed in [TT]chi.log[tt] as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
};
/* defaults */
static int r0=1,ndeg=1,maxchi=2;
static gmx_bool bAll=FALSE;
static gmx_bool bPhi=FALSE,bPsi=FALSE,bOmega=FALSE;
static real bfac_init=-1.0,bfac_max=0;
static const char *maxchistr[] = { NULL, "0", "1", "2", "3", "4", "5", "6", NULL };
static gmx_bool bRama=FALSE,bShift=FALSE,bViol=FALSE,bRamOmega=FALSE;
static gmx_bool bNormHisto=TRUE,bChiProduct=FALSE,bHChi=FALSE,bRAD=FALSE,bPBC=TRUE;
static real core_frac=0.5 ;
t_pargs pa[] = {
{ "-r0", FALSE, etINT, {&r0},
"starting residue" },
{ "-phi", FALSE, etBOOL, {&bPhi},
"Output for [GRK]phi[grk] dihedral angles" },
{ "-psi", FALSE, etBOOL, {&bPsi},
"Output for [GRK]psi[grk] dihedral angles" },
{ "-omega",FALSE, etBOOL, {&bOmega},
"Output for [GRK]omega[grk] dihedrals (peptide bonds)" },
{ "-rama", FALSE, etBOOL, {&bRama},
"Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots" },
{ "-viol", FALSE, etBOOL, {&bViol},
"Write a file that gives 0 or 1 for violated Ramachandran angles" },
{ "-periodic", FALSE, etBOOL, {&bPBC},
"Print dihedral angles modulo 360 degrees" },
{ "-all", FALSE, etBOOL, {&bAll},
"Output separate files for every dihedral." },
{ "-rad", FALSE, etBOOL, {&bRAD},
"in angle vs time files, use radians rather than degrees."},
{ "-shift", FALSE, etBOOL, {&bShift},
"Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles" },
{ "-binwidth", FALSE, etINT, {&ndeg},
"bin width for histograms (degrees)" },
{ "-core_rotamer", FALSE, etREAL, {&core_frac},
"only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
{ "-maxchi", FALSE, etENUM, {maxchistr},
"calculate first ndih [GRK]chi[grk] dihedrals" },
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Normalize histograms" },
{ "-ramomega",FALSE,etBOOL, {&bRamOmega},
"compute average omega as a function of phi/psi and plot it in an [TT].xpm[tt] plot" },
{ "-bfact", FALSE, etREAL, {&bfac_init},
"B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
{ "-chi_prod",FALSE,etBOOL, {&bChiProduct},
"compute a single cumulative rotamer for each residue"},
{ "-HChi",FALSE,etBOOL, {&bHChi},
"Include dihedrals to sidechain hydrogens"},
{ "-bmax", FALSE, etREAL, {&bfac_max},
"Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. [TT]-bmax[tt] <= 0 means no limit." }
};
FILE *log;
int natoms,nlist,idum,nbin;
t_atoms atoms;
rvec *x;
int ePBC;
matrix box;
char title[256],grpname[256];
t_dlist *dlist;
gmx_bool bChi,bCorr,bSSHisto;
gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc ;
real dt=0, traj_t_ns;
output_env_t oenv;
gmx_residuetype_t rt;
atom_id isize,*index;
int ndih,nactdih,nf;
real **dih,*trans_frac,*aver_angle,*time;
int i,j,**chi_lookup,*xity;
t_filenm fnm[] = {
{ efSTX, "-s", NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-o", "order", ffWRITE },
{ efPDB, "-p", "order", ffOPTWR },
{ efDAT, "-ss", "ssdump", ffOPTRD },
{ efXVG, "-jc", "Jcoupling", ffWRITE },
{ efXVG, "-corr", "dihcorr",ffOPTWR },
{ efLOG, "-g", "chi", ffWRITE },
/* add two more arguments copying from g_angle */
{ efXVG, "-ot", "dihtrans", ffOPTWR },
{ efXVG, "-oh", "trhisto", ffOPTWR },
{ efXVG, "-rt", "restrans", ffOPTWR },
{ efXVG, "-cp", "chiprodhisto", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs,
&oenv);
/* Handle result from enumerated type */
sscanf(maxchistr[0],"%d",&maxchi);
bChi = (maxchi > 0);
log=ffopen(ftp2fn(efLOG,NFILE,fnm),"w");
if (bRamOmega) {
bOmega = TRUE;
bPhi = TRUE;
bPsi = TRUE;
}
/* set some options */
bDo_rt=(opt2bSet("-rt",NFILE,fnm));
bDo_oh=(opt2bSet("-oh",NFILE,fnm));
bDo_ot=(opt2bSet("-ot",NFILE,fnm));
bDo_jc=(opt2bSet("-jc",NFILE,fnm));
bCorr=(opt2bSet("-corr",NFILE,fnm));
if (bCorr)
fprintf(stderr,"Will calculate autocorrelation\n");
if (core_frac > 1.0 ) {
fprintf(stderr, "core_rotamer fraction > 1.0 ; will use 1.0\n");
core_frac=1.0 ;
}
if (core_frac < 0.0 ) {
fprintf(stderr, "core_rotamer fraction < 0.0 ; will use 0.0\n");
core_frac=0.0 ;
}
if (maxchi > MAXCHI) {
fprintf(stderr,
"Will only calculate first %d Chi dihedrals in stead of %d.\n",
MAXCHI, maxchi);
maxchi=MAXCHI;
}
bSSHisto = ftp2bSet(efDAT,NFILE,fnm);
nbin = 360/ndeg ;
/* Find the chi angles using atoms struct and a list of amino acids */
get_stx_coordnum(ftp2fn(efSTX,NFILE,fnm),&natoms);
init_t_atoms(&atoms,natoms,TRUE);
snew(x,natoms);
read_stx_conf(ftp2fn(efSTX,NFILE,fnm),title,&atoms,x,NULL,&ePBC,box);
fprintf(log,"Title: %s\n",title);
gmx_residuetype_init(&rt);
dlist=mk_dlist(log,&atoms,&nlist,bPhi,bPsi,bChi,bHChi,maxchi,r0,rt);
fprintf(stderr,"%d residues with dihedrals found\n", nlist);
if (nlist == 0)
gmx_fatal(FARGS,"No dihedrals in your structure!\n");
/* Make a linear index for reading all. */
index=make_chi_ind(nlist,dlist,&ndih);
isize=4*ndih;
fprintf(stderr,"%d dihedrals found\n", ndih);
snew(dih,ndih);
/* COMPUTE ALL DIHEDRALS! */
read_ang_dih(ftp2fn(efTRX,NFILE,fnm),FALSE,TRUE,FALSE,bPBC,1,&idum,
&nf,&time,isize,index,&trans_frac,&aver_angle,dih,oenv);
dt=(time[nf-1]-time[0])/(nf-1); /* might want this for corr or n. transit*/
if (bCorr)
{
if (nf < 2)
{
gmx_fatal(FARGS,"Need at least 2 frames for correlation");
}
}
/* put angles in -M_PI to M_PI ! and correct phase factor for phi and psi
* pass nactdih instead of ndih to low_ana_dih_trans and get_chi_product_traj
* to prevent accessing off end of arrays when maxchi < 5 or 6. */
nactdih = reset_em_all(nlist,dlist,nf,dih,maxchi);
if (bAll)
dump_em_all(nlist,dlist,nf,time,dih,maxchi,bPhi,bPsi,bChi,bOmega,bRAD,oenv);
/* Histogramming & J coupling constants & calc of S2 order params */
histogramming(log,nbin,rt,nf,maxchi,dih,nlist,dlist,index,
bPhi,bPsi,bOmega,bChi,
bNormHisto,bSSHisto,ftp2fn(efDAT,NFILE,fnm),bfac_max,&atoms,
bDo_jc,opt2fn("-jc",NFILE,fnm),oenv);
/* transitions
*
* added multiplicity */
snew(xity,ndih) ;
mk_multiplicity_lookup(xity, maxchi, dih, nlist, dlist,ndih);
strcpy(grpname, "All residues, ");
if(bPhi)
strcat(grpname, "Phi ");
if(bPsi)
strcat(grpname, "Psi ");
if(bOmega)
strcat(grpname, "Omega ");
if(bChi){
strcat(grpname, "Chi 1-") ;
sprintf(grpname + strlen(grpname), "%i", maxchi);
}
low_ana_dih_trans(bDo_ot, opt2fn("-ot",NFILE,fnm),
bDo_oh, opt2fn("-oh",NFILE,fnm),maxchi,
dih, nlist, dlist, nf, nactdih, grpname, xity,
*time, dt, FALSE, core_frac,oenv) ;
/* Order parameters */
order_params(log,opt2fn("-o",NFILE,fnm),maxchi,nlist,dlist,
ftp2fn_null(efPDB,NFILE,fnm),bfac_init,
&atoms,x,ePBC,box,bPhi,bPsi,bChi,oenv);
/* Print ramachandran maps! */
if (bRama)
do_rama(nf,nlist,dlist,dih,bViol,bRamOmega,oenv);
if (bShift)
do_pp2shifts(log,nf,nlist,dlist,dih);
/* rprint S^2, transitions, and rotamer occupancies to log */
traj_t_ns = 0.001 * (time[nf-1]-time[0]) ;
pr_dlist(log,nlist,dlist,traj_t_ns,edPrintST,bPhi,bPsi,bChi,bOmega,maxchi);
pr_dlist(log,nlist,dlist,traj_t_ns,edPrintRO,bPhi,bPsi,bChi,bOmega,maxchi);
ffclose(log);
/* transitions to xvg */
if (bDo_rt)
print_transitions(opt2fn("-rt",NFILE,fnm),maxchi,nlist,dlist,
&atoms,x,box,bPhi,bPsi,bChi,traj_t_ns,oenv);
/* chi_product trajectories (ie one "rotamer number" for each residue) */
if (bChiProduct && bChi ) {
snew(chi_lookup,nlist) ;
for (i=0;i<nlist;i++)
snew(chi_lookup[i], maxchi) ;
mk_chi_lookup(chi_lookup, maxchi, dih, nlist, dlist);
get_chi_product_traj(dih,nf,nactdih,nlist,
maxchi,dlist,time,chi_lookup,xity,
FALSE,bNormHisto, core_frac,bAll,
opt2fn("-cp",NFILE,fnm),oenv);
for (i=0;i<nlist;i++)
sfree(chi_lookup[i]);
}
/* Correlation comes last because it f***s up the angles */
if (bCorr)
do_dihcorr(opt2fn("-corr",NFILE,fnm),nf,ndih,dih,dt,nlist,dlist,time,
maxchi,bPhi,bPsi,bChi,bOmega,oenv);
do_view(oenv,opt2fn("-o",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-jc",NFILE,fnm),"-nxy");
if (bCorr)
do_view(oenv,opt2fn("-corr",NFILE,fnm),"-nxy");
gmx_residuetype_destroy(rt);
thanx(stderr);
return 0;
}
int gmx_rmsf(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the root mean square fluctuation (RMSF, i.e. standard ",
"deviation) of atomic positions in the trajectory (supplied with [TT]-f[tt])",
"after (optionally) fitting to a reference frame (supplied with [TT]-s[tt]).[PAR]",
"With option [TT]-oq[tt] the RMSF values are converted to B-factor",
"values, which are written to a [TT].pdb[tt] file with the coordinates, of the",
"structure file, or of a [TT].pdb[tt] file when [TT]-q[tt] is specified.",
"Option [TT]-ox[tt] writes the B-factors to a file with the average",
"coordinates.[PAR]",
"With the option [TT]-od[tt] the root mean square deviation with",
"respect to the reference structure is calculated.[PAR]",
"With the option [TT]-aniso[tt], [THISMODULE] will compute anisotropic",
"temperature factors and then it will also output average coordinates",
"and a [TT].pdb[tt] file with ANISOU records (corresonding to the [TT]-oq[tt]",
"or [TT]-ox[tt] option). Please note that the U values",
"are orientation-dependent, so before comparison with experimental data",
"you should verify that you fit to the experimental coordinates.[PAR]",
"When a [TT].pdb[tt] input file is passed to the program and the [TT]-aniso[tt]",
"flag is set",
"a correlation plot of the Uij will be created, if any anisotropic",
"temperature factors are present in the [TT].pdb[tt] file.[PAR]",
"With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
"This shows the directions in which the atoms fluctuate the most and",
"the least."
};
static gmx_bool bRes = FALSE, bAniso = FALSE, bdevX = FALSE, bFit = TRUE;
t_pargs pargs[] = {
{ "-res", FALSE, etBOOL, {&bRes},
"Calculate averages for each residue" },
{ "-aniso", FALSE, etBOOL, {&bAniso},
"Compute anisotropic termperature factors" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match." }
};
int natom;
int step, nre, natoms, i, g, m, teller = 0;
real t, lambda, *w_rls, *w_rms;
t_tpxheader header;
t_inputrec ir;
t_topology top;
int ePBC;
t_atoms *pdbatoms, *refatoms;
gmx_bool bCont;
matrix box, pdbbox;
rvec *x, *pdbx, *xref;
t_trxstatus *status;
int npdbatoms, res0;
char buf[256];
const char *label;
char title[STRLEN];
FILE *fp; /* the graphics file */
const char *devfn, *dirfn;
int resind;
gmx_bool bReadPDB;
atom_id *index;
int isize;
char *grpnames;
real bfac, pdb_bfac, *Uaver;
double **U, *xav;
atom_id aid;
rvec *rmsd_x = NULL;
double *rmsf, invcount, totmass;
int d;
real count = 0;
rvec xcm;
gmx_rmpbc_t gpbc = NULL;
output_env_t oenv;
const char *leg[2] = { "MD", "X-Ray" };
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efPDB, "-q", NULL, ffOPTRD },
{ efPDB, "-oq", "bfac", ffOPTWR },
{ efPDB, "-ox", "xaver", ffOPTWR },
{ efXVG, "-o", "rmsf", ffWRITE },
{ efXVG, "-od", "rmsdev", ffOPTWR },
{ efXVG, "-oc", "correl", ffOPTWR },
{ efLOG, "-dir", "rmsf", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
&oenv))
{
return 0;
}
bReadPDB = ftp2bSet(efPDB, NFILE, fnm);
devfn = opt2fn_null("-od", NFILE, fnm);
dirfn = opt2fn_null("-dir", NFILE, fnm);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xref, NULL, box, TRUE);
snew(w_rls, top.atoms.nr);
fprintf(stderr, "Select group(s) for root mean square calculation\n");
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpnames);
/* Set the weight */
for (i = 0; i < isize; i++)
{
w_rls[index[i]] = top.atoms.atom[index[i]].m;
}
/* Malloc the rmsf arrays */
snew(xav, isize*DIM);
snew(U, isize);
for (i = 0; i < isize; i++)
{
snew(U[i], DIM*DIM);
}
snew(rmsf, isize);
if (devfn)
{
snew(rmsd_x, isize);
}
if (bReadPDB)
{
get_stx_coordnum(opt2fn("-q", NFILE, fnm), &npdbatoms);
snew(pdbatoms, 1);
snew(refatoms, 1);
init_t_atoms(pdbatoms, npdbatoms, TRUE);
init_t_atoms(refatoms, npdbatoms, TRUE);
snew(pdbx, npdbatoms);
/* Read coordinates twice */
read_stx_conf(opt2fn("-q", NFILE, fnm), title, pdbatoms, pdbx, NULL, NULL, pdbbox);
read_stx_conf(opt2fn("-q", NFILE, fnm), title, refatoms, pdbx, NULL, NULL, pdbbox);
}
else
{
pdbatoms = &top.atoms;
refatoms = &top.atoms;
pdbx = xref;
npdbatoms = pdbatoms->nr;
snew(pdbatoms->pdbinfo, npdbatoms);
copy_mat(box, pdbbox);
}
if (bFit)
{
sub_xcm(xref, isize, index, top.atoms.atom, xcm, FALSE);
}
natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
if (bFit)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natom);
}
/* Now read the trj again to compute fluctuations */
teller = 0;
do
{
if (bFit)
{
/* Remove periodic boundary */
gmx_rmpbc(gpbc, natom, box, x);
/* Set center of mass to zero */
sub_xcm(x, isize, index, top.atoms.atom, xcm, FALSE);
/* Fit to reference structure */
do_fit(natom, w_rls, xref, x);
}
/* Calculate Anisotropic U Tensor */
for (i = 0; i < isize; i++)
{
aid = index[i];
for (d = 0; d < DIM; d++)
{
xav[i*DIM + d] += x[aid][d];
for (m = 0; m < DIM; m++)
{
U[i][d*DIM + m] += x[aid][d]*x[aid][m];
}
}
}
if (devfn)
{
/* Calculate RMS Deviation */
for (i = 0; (i < isize); i++)
{
aid = index[i];
for (d = 0; (d < DIM); d++)
{
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (bFit)
{
gmx_rmpbc_done(gpbc);
}
invcount = 1.0/count;
snew(Uaver, DIM*DIM);
totmass = 0;
for (i = 0; i < isize; i++)
{
for (d = 0; d < DIM; d++)
{
xav[i*DIM + d] *= invcount;
}
for (d = 0; d < DIM; d++)
{
for (m = 0; m < DIM; m++)
{
U[i][d*DIM + m] = U[i][d*DIM + m]*invcount
- xav[i*DIM + d]*xav[i*DIM + m];
Uaver[3*d+m] += top.atoms.atom[index[i]].m*U[i][d*DIM + m];
}
}
totmass += top.atoms.atom[index[i]].m;
}
for (d = 0; d < DIM*DIM; d++)
{
Uaver[d] /= totmass;
}
if (bRes)
{
for (d = 0; d < DIM*DIM; d++)
{
average_residues(NULL, U, d, isize, index, w_rls, &top.atoms);
}
}
if (bAniso)
{
for (i = 0; i < isize; i++)
{
aid = index[i];
pdbatoms->pdbinfo[aid].bAnisotropic = TRUE;
pdbatoms->pdbinfo[aid].uij[U11] = 1e6*U[i][XX*DIM + XX];
pdbatoms->pdbinfo[aid].uij[U22] = 1e6*U[i][YY*DIM + YY];
pdbatoms->pdbinfo[aid].uij[U33] = 1e6*U[i][ZZ*DIM + ZZ];
pdbatoms->pdbinfo[aid].uij[U12] = 1e6*U[i][XX*DIM + YY];
pdbatoms->pdbinfo[aid].uij[U13] = 1e6*U[i][XX*DIM + ZZ];
pdbatoms->pdbinfo[aid].uij[U23] = 1e6*U[i][YY*DIM + ZZ];
}
}
if (bRes)
{
label = "Residue";
}
else
{
label = "Atom";
}
for (i = 0; i < isize; i++)
{
rmsf[i] = U[i][XX*DIM + XX] + U[i][YY*DIM + YY] + U[i][ZZ*DIM + ZZ];
}
if (dirfn)
{
fprintf(stdout, "\n");
print_dir(stdout, Uaver);
fp = gmx_ffopen(dirfn, "w");
print_dir(fp, Uaver);
gmx_ffclose(fp);
}
for (i = 0; i < isize; i++)
{
sfree(U[i]);
}
sfree(U);
/* Write RMSF output */
if (bReadPDB)
{
bfac = 8.0*M_PI*M_PI/3.0*100;
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "B-Factors",
label, "(A\\b\\S\\So\\N\\S2\\N)", oenv);
xvgr_legend(fp, 2, leg, oenv);
for (i = 0; (i < isize); i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
resind = top.atoms.atom[index[i]].resind;
pdb_bfac = find_pdb_bfac(pdbatoms, &top.atoms.resinfo[resind],
*(top.atoms.atomname[index[i]]));
fprintf(fp, "%5d %10.5f %10.5f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, rmsf[i]*bfac,
pdb_bfac);
}
}
gmx_ffclose(fp);
}
else
{
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS fluctuation", label, "(nm)", oenv);
for (i = 0; i < isize; i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
fprintf(fp, "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
}
}
gmx_ffclose(fp);
}
for (i = 0; i < isize; i++)
{
pdbatoms->pdbinfo[index[i]].bfac = 800*M_PI*M_PI/3.0*rmsf[i];
}
if (devfn)
{
for (i = 0; i < isize; i++)
{
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
}
if (bRes)
{
average_residues(rmsf, NULL, 0, isize, index, w_rls, &top.atoms);
}
/* Write RMSD output */
fp = xvgropen(devfn, "RMS Deviation", label, "(nm)", oenv);
for (i = 0; i < isize; i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
fprintf(fp, "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
}
}
gmx_ffclose(fp);
}
if (opt2bSet("-oq", NFILE, fnm))
{
/* Write a .pdb file with B-factors and optionally anisou records */
for (i = 0; i < isize; i++)
{
rvec_inc(xref[index[i]], xcm);
}
write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx,
NULL, ePBC, pdbbox, isize, index);
}
if (opt2bSet("-ox", NFILE, fnm))
{
/* Misuse xref as a temporary array */
for (i = 0; i < isize; i++)
{
for (d = 0; d < DIM; d++)
{
xref[index[i]][d] = xcm[d] + xav[i*DIM + d];
}
}
/* Write a .pdb file with B-factors and optionally anisou records */
write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, xref, NULL,
ePBC, pdbbox, isize, index);
}
if (bAniso)
{
correlate_aniso(opt2fn("-oc", NFILE, fnm), refatoms, pdbatoms, oenv);
do_view(oenv, opt2fn("-oc", NFILE, fnm), "-nxy");
}
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
if (devfn)
{
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
}
return 0;
}
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;
}
static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **r,
int ePBC, matrix box,
gmx_atomprop_t aps, real r_distance, int *atoms_added,
int *residues_added, real rshell, int max_sol,
const output_env_t oenv)
{
int i, nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt, *v_solvt = NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr, onres;
char *lfn;
lfn = gmxlibfn(fn);
strncpy(filename, lfn, STRLEN);
sfree(lfn);
snew(atoms_solvt, 1);
get_stx_coordnum(filename, &(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
{
gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
}
snew(x_solvt, atoms_solvt->nr);
if (v)
{
snew(v_solvt, atoms_solvt->nr);
}
snew(r_solvt, atoms_solvt->nr);
snew(atoms_solvt->resinfo, atoms_solvt->nr);
snew(atoms_solvt->atomname, atoms_solvt->nr);
snew(atoms_solvt->atom, atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr, "Reading solvent configuration%s\n",
v_solvt ? " and velocities" : "");
read_stx_conf(filename, title_solvt, atoms_solvt, x_solvt, v_solvt,
&ePBC_solvt, box_solvt);
fprintf(stderr, "\"%s\"\n", title_solvt);
fprintf(stderr, "solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr, atoms_solvt->nres);
fprintf(stderr, "\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt, r_solvt, aps, r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol = 1;
for (i = 0; (i < DIM); i++)
{
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
{
n_box[i]++;
}
nmol *= n_box[i];
}
fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX], n_box[YY], n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resinfo, atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname, atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom, atoms_solvt->nr*nmol);
srenew(x_solvt, atoms_solvt->nr*nmol);
if (v_solvt)
{
srenew(v_solvt, atoms_solvt->nr*nmol);
}
srenew(r_solvt, atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt, x_solvt, v_solvt, r_solvt, box_solvt, n_box);
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt, x_solvt, v_solvt, r_solvt);
/* add the two configurations */
onr = atoms->nr;
onres = atoms->nres;
add_conf(atoms, x, v, r, TRUE, ePBC, box, FALSE,
atoms_solvt, x_solvt, v_solvt, r_solvt, TRUE, rshell, max_sol, oenv);
*atoms_added = atoms->nr-onr;
*residues_added = atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
*atoms_added, *residues_added);
}
static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
gmx_atomprop_t aps,
real r_distance, real r_scale, real rshell,
const output_env_t oenv,
const char* posfn, const rvec deltaR, int enum_rot,
gmx_bool bCheckAllPairDist)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt, *x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i, mol, onr, ncol;
real alfa = 0., beta = 0., gamma = 0.;
rvec offset_x;
int trial;
double **rpos;
set_pbc(&pbc, ePBC, box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
if (atoms_insrt.nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
}
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt, atoms_insrt.nr);
snew(r_insrt, atoms_insrt.nr);
snew(atoms_insrt.resinfo, atoms_insrt.nr);
snew(atoms_insrt.atomname, atoms_insrt.nr);
snew(atoms_insrt.atom, atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n, atoms_insrt.nr);
snew(title_insrt, STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr, "Reading molecule configuration \n");
read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
&ePBC_insrt, box_insrt);
fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
title_insrt, atoms_insrt.nr, atoms_insrt.nres);
srenew(atoms_insrt.resinfo, atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt, r_insrt, aps, r_distance, r_scale);
/* With -ip, take nmol_insrt from file posfn */
if (posfn != NULL)
{
nmol_insrt = read_xvg(posfn, &rpos, &ncol);
if (ncol != 3)
{
gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
}
fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
}
srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
trial = mol = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
fprintf(stderr, "\rTry %d", trial++);
for (i = 0; (i < atoms_insrt.nr); i++)
{
copy_rvec(x_insrt[i], x_n[i]);
}
switch (enum_rot)
{
case en_rotXYZ:
alfa = 2*M_PI *rando(&seed);
beta = 2*M_PI *rando(&seed);
gamma = 2*M_PI *rando(&seed);
break;
case en_rotZ:
alfa = beta = 0.;
gamma = 2*M_PI*rando(&seed);
break;
case en_rotNone:
alfa = beta = gamma = 0.;
break;
}
if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
{
rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
}
if (posfn == NULL)
{
/* insert at random positions */
offset_x[XX] = box[XX][XX]*rando(&seed);
offset_x[YY] = box[YY][YY]*rando(&seed);
offset_x[ZZ] = box[ZZ][ZZ]*rando(&seed);
gen_box(0, atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
{
continue;
}
}
else
{
/* Insert at positions taken from option -ip file */
offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2*rando(&seed)-1);
offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2*rando(&seed)-1);
offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2*rando(&seed)-1);
for (i = 0; i < atoms_insrt.nr; i++)
{
rvec_inc(x_n[i], offset_x);
}
}
onr = atoms->nr;
/* This is a (maybe) slow workaround to avoid too many calls of add_conf, which
* leaks memory (status May 2012). If the momory leaks in add_conf() are fixed,
* this check could be removed. Note, however, that allPairsDistOk is probably
* even faster than add_conf() when inserting a small molecule into a moderately
* small system.
*/
if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *r, ePBC, box, &atoms_insrt, x_n, r_insrt))
{
continue;
}
add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
&atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
if (atoms->nr == (atoms_insrt.nr+onr))
{
mol++;
fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
}
}
srenew(atoms->resinfo, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
return title_insrt;
}
static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
gmx_atomprop_t aps, real r_distance, real rshell,
const output_env_t oenv)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt, *x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i, mol, onr;
real alfa, beta, gamma;
rvec offset_x;
int trial;
set_pbc(&pbc, ePBC, box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
if (atoms_insrt.nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
}
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt, atoms_insrt.nr);
snew(r_insrt, atoms_insrt.nr);
snew(atoms_insrt.resinfo, atoms_insrt.nr);
snew(atoms_insrt.atomname, atoms_insrt.nr);
snew(atoms_insrt.atom, atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n, atoms_insrt.nr);
snew(title_insrt, STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr, "Reading molecule configuration \n");
read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
&ePBC_insrt, box_insrt);
fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
title_insrt, atoms_insrt.nr, atoms_insrt.nres);
srenew(atoms_insrt.resinfo, atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt, r_insrt, aps, r_distance);
srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
trial = mol = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
fprintf(stderr, "\rTry %d", trial++);
for (i = 0; (i < atoms_insrt.nr); i++)
{
copy_rvec(x_insrt[i], x_n[i]);
}
alfa = 2*M_PI*rando( &seed);
beta = 2*M_PI*rando( &seed);
gamma = 2*M_PI*rando( &seed);
rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
offset_x[XX] = box[XX][XX]*rando(&seed);
offset_x[YY] = box[YY][YY]*rando(&seed);
offset_x[ZZ] = box[ZZ][ZZ]*rando(&seed);
gen_box(0, atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
{
continue;
}
onr = atoms->nr;
add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
&atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
if (atoms->nr == (atoms_insrt.nr+onr))
{
mol++;
fprintf(stderr, " success (now %d atoms)!", atoms->nr);
}
}
srenew(atoms->resinfo, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
return title_insrt;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"compnl compares two neighborlists as generated by [TT]mdrun[tt]",
"in the log file, when the environment variable DUMPNL is set to",
"a number larger than 0. compnl is mainly used for debugging the",
"mdrun internals and not for end-users."
};
FILE *in,*out;
int i,j,nmiss,mod;
char **fn,title[256];
int ***mat,nnb;
real mb;
bool bConf;
rvec *x = NULL;
rvec dx;
matrix box;
t_atoms atoms;
t_pbc pbc;
t_filenm fnm[] = {
{ efLOG, "-f1", NULL, ffREAD },
{ efLOG, "-f2", NULL, ffREAD },
{ efOUT, "-o", "compnl", ffWRITE },
{ efSTX, "-c", NULL, ffOPTRD }
};
#define NFILE asize(fnm)
static int natoms=648;
static bool bSymm=TRUE;
static t_pargs pa[] = {
{ "-nat", FALSE, etINT, { &natoms }, "Number of atoms" },
{ "-symm", FALSE, etBOOL,{ &bSymm }, "Symmetrize the matrices" },
};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
bConf = (opt2bSet("-c",NFILE,fnm));
if (bConf) {
get_stx_coordnum (opt2fn("-c",NFILE,fnm),&natoms);
init_t_atoms(&atoms,natoms,FALSE);
snew(x,natoms);
read_stx_conf(opt2fn("-c",NFILE,fnm),title,&atoms,x,NULL,box);
set_pbc(&pbc,box);
}
snew(fn,2);
fn[0] = opt2fn("-f1",NFILE,fnm);
fn[1] = opt2fn("-f2",NFILE,fnm);
snew(mat,2);
out = gmx_fio_fopen(ftp2fn(efOUT,NFILE,fnm),"w");
mb = sizeof(int)*sqr(natoms/1024.0);
for(i=0; (i<2); i++) {
in = gmx_fio_fopen(fn[i],"r");
fprintf(stderr,"Reading %s\n",fn[i]);
fprintf(out, "Reading %s\n",fn[i]);
fprintf(stderr,"Going to allocate %.0f Mb of memory\n",mb);
fprintf(out, "Going to allocate %.0f Mb of memory\n",mb);
snew(mat[i],natoms);
for(j=0; (j<natoms); j++)
snew(mat[i][j],natoms);
nnb = read_nblist(in,out,mat[i],natoms,bSymm);
gmx_fio_fclose(in);
fprintf(stderr,"Interaction matrix %d has %d entries\n",i,nnb);
fprintf(out, "Interaction matrix %d has %d entries\n",i,nnb);
}
fprintf(stderr,"Comparing Interaction Matrices\n");
mod=1;
nmiss = 0;
for(i=0; (i<natoms); i+=mod) {
for(j=0; (j<natoms); j+=mod) {
if (mat[0][i][j] != mat[1][i][j]) {
fprintf(out,"i: %5d, j: %5d, shift[%s]: %3d, shift[%s]: %3d",
i,j,fn[0],mat[0][i][j]-1,fn[1],mat[1][i][j]-1);
if (bConf) {
pbc_dx(&pbc,x[i],x[j],dx);
fprintf(out," dist: %8.3f\n",norm(dx));
}
else
fprintf(out,"\n");
nmiss++;
}
}
}
fprintf(out,"There were %d mismatches\n",nmiss);
fprintf(out,"Done.\n");
gmx_fio_fclose(out);
fprintf(stderr,"There were %d mismatches\n",nmiss);
fprintf(stderr,"Finished\n");
thanx(stdout);
return 0;
}
int gmx_make_ndx(int argc, char *argv[])
{
const char *desc[] = {
"Index groups are necessary for almost every GROMACS program.",
"All these programs can generate default index groups. You ONLY",
"have to use [THISMODULE] when you need SPECIAL index groups.",
"There is a default index group for the whole system, 9 default",
"index groups for proteins, and a default index group",
"is generated for every other residue name.[PAR]",
"When no index file is supplied, also [THISMODULE] will generate the",
"default groups.",
"With the index editor you can select on atom, residue and chain names",
"and numbers.",
"When a run input file is supplied you can also select on atom type.",
"You can use NOT, AND and OR, you can split groups",
"into chains, residues or atoms. You can delete and rename groups.[PAR]",
"The atom numbering in the editor and the index file starts at 1.[PAR]",
"The [TT]-twin[tt] switch duplicates all index groups with an offset of",
"[TT]-natoms[tt], which is useful for Computational Electrophysiology",
"double-layer membrane setups."
};
static int natoms = 0;
static gmx_bool bVerbose = FALSE;
static gmx_bool bDuplicate = FALSE;
t_pargs pa[] = {
{ "-natoms", FALSE, etINT, {&natoms},
"set number of atoms (default: read from coordinate or index file)" },
{ "-twin", FALSE, etBOOL, {&bDuplicate},
"Duplicate all index groups with an offset of -natoms" },
{ "-verbose", FALSE, etBOOL, {&bVerbose},
"HIDDENVerbose output" }
};
#define NPA asize(pa)
output_env_t oenv;
char title[STRLEN];
int nndxin;
const char *stxfile;
char **ndxinfiles;
const char *ndxoutfile;
gmx_bool bNatoms;
int i, j;
t_atoms *atoms;
rvec *x, *v;
int ePBC;
matrix box;
t_blocka *block, *block2;
char **gnames, **gnames2;
t_filenm fnm[] = {
{ efSTX, "-f", NULL, ffOPTRD },
{ efNDX, "-n", NULL, ffOPTRDMULT },
{ efNDX, "-o", NULL, ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv))
{
return 0;
}
stxfile = ftp2fn_null(efSTX, NFILE, fnm);
if (opt2bSet("-n", NFILE, fnm))
{
nndxin = opt2fns(&ndxinfiles, "-n", NFILE, fnm);
}
else
{
nndxin = 0;
}
ndxoutfile = opt2fn("-o", NFILE, fnm);
bNatoms = opt2parg_bSet("-natoms", NPA, pa);
if (!stxfile && !nndxin)
{
gmx_fatal(FARGS, "No input files (structure or index)");
}
if (stxfile)
{
snew(atoms, 1);
get_stx_coordnum(stxfile, &(atoms->nr));
init_t_atoms(atoms, atoms->nr, TRUE);
snew(x, atoms->nr);
snew(v, atoms->nr);
fprintf(stderr, "\nReading structure file\n");
read_stx_conf(stxfile, title, atoms, x, v, &ePBC, box);
natoms = atoms->nr;
bNatoms = TRUE;
}
else
{
atoms = NULL;
x = NULL;
}
/* read input file(s) */
block = new_blocka();
gnames = NULL;
printf("Going to read %d old index file(s)\n", nndxin);
if (nndxin)
{
for (i = 0; i < nndxin; i++)
{
block2 = init_index(ndxinfiles[i], &gnames2);
srenew(gnames, block->nr+block2->nr);
for (j = 0; j < block2->nr; j++)
{
gnames[block->nr+j] = gnames2[j];
}
sfree(gnames2);
merge_blocks(block, block2);
sfree(block2->a);
sfree(block2->index);
/* done_block(block2); */
sfree(block2);
}
}
else
{
snew(gnames, 1);
analyse(atoms, block, &gnames, FALSE, TRUE);
}
if (!bNatoms)
{
natoms = block2natoms(block);
printf("Counted atom numbers up to %d in index file\n", natoms);
}
edit_index(natoms, atoms, x, block, &gnames, bVerbose);
write_index(ndxoutfile, block, gnames, bDuplicate, natoms);
return 0;
}
static void
new_status(char *topfile,char *topppfile,char *confin,
t_gromppopts *opts,t_inputrec *ir,bool bZero,
bool bGenVel,bool bVerbose,t_state *state,
gpp_atomtype_t atype,gmx_mtop_t *sys,
int *nmi,t_molinfo **mi,t_params plist[],
int *comb,double *reppow,real *fudgeQQ,
bool bMorse,
int *nerror)
{
t_molinfo *molinfo=NULL;
int nmolblock;
gmx_molblock_t *molblock,*molbs;
t_atoms *confat;
int mb,mbs,i,nrmols,nmismatch;
char buf[STRLEN];
bool bGB=FALSE;
init_mtop(sys);
/* Set boolean for GB */
if(ir->implicit_solvent)
bGB=TRUE;
/* TOPOLOGY processing */
sys->name = do_top(bVerbose,topfile,topppfile,opts,bZero,&(sys->symtab),
plist,comb,reppow,fudgeQQ,
atype,&nrmols,&molinfo,ir,
&nmolblock,&molblock,bGB);
sys->nmolblock = 0;
snew(sys->molblock,nmolblock);
mbs;
sys->natoms = 0;
for(mb=0; mb<nmolblock; mb++) {
if (sys->nmolblock > 0 &&
molblock[mb].type == sys->molblock[sys->nmolblock-1].type) {
/* Merge consecutive blocks with the same molecule type */
sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
} else if (molblock[mb].nmol > 0) {
/* Add a new molblock to the topology */
molbs = &sys->molblock[sys->nmolblock];
*molbs = molblock[mb];
molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
molbs->nposres_xA = 0;
molbs->nposres_xB = 0;
sys->natoms += molbs->nmol*molbs->natoms_mol;
sys->nmolblock++;
}
}
if (sys->nmolblock == 0) {
gmx_fatal(FARGS,"No molecules were defined in the system");
}
renumber_moltypes(sys,&nrmols,&molinfo);
if (bMorse)
convert_harmonics(nrmols,molinfo,atype);
if (ir->eDisre == edrNone) {
i = rm_interactions(F_DISRES,nrmols,molinfo);
if (i > 0) {
set_warning_line("unknown",-1);
sprintf(warn_buf,"disre = no, removed %d distance restraints",i);
warning_note(NULL);
}
}
if (opts->bOrire == FALSE) {
i = rm_interactions(F_ORIRES,nrmols,molinfo);
if (i > 0) {
set_warning_line("unknown",-1);
sprintf(warn_buf,"orire = no, removed %d orientation restraints",i);
warning_note(NULL);
}
}
if (opts->bDihre == FALSE) {
i = rm_interactions(F_DIHRES,nrmols,molinfo);
if (i > 0) {
set_warning_line("unknown",-1);
sprintf(warn_buf,"dihre = no, removed %d dihedral restraints",i);
warning_note(NULL);
}
}
/* Copy structures from msys to sys */
molinfo2mtop(nrmols,molinfo,sys);
/* COORDINATE file processing */
if (bVerbose)
fprintf(stderr,"processing coordinates...\n");
get_stx_coordnum(confin,&state->natoms);
if (state->natoms != sys->natoms)
gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (%s, %d)",
confin,state->natoms,topfile,sys->natoms);
else {
/* make space for coordinates and velocities */
char title[STRLEN];
snew(confat,1);
init_t_atoms(confat,state->natoms,FALSE);
init_state(state,state->natoms,0);
read_stx_conf(confin,title,confat,state->x,state->v,NULL,state->box);
/* This call fixes the box shape for runs with pressure scaling */
set_box_rel(ir,state);
nmismatch = check_atom_names(topfile, confin, sys, confat);
free_t_atoms(confat,TRUE);
sfree(confat);
if (nmismatch) {
sprintf(buf,"%d non-matching atom name%s\n"
"atom names from %s will be used\n"
"atom names from %s will be ignored\n",
nmismatch,(nmismatch == 1) ? "" : "s",topfile,confin);
warning(buf);
}
if (bVerbose)
fprintf(stderr,"double-checking input for internal consistency...\n");
double_check(ir,state->box,nint_ftype(sys,molinfo,F_CONSTR),nerror);
}
if (bGenVel) {
real *mass;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
snew(mass,state->natoms);
aloop = gmx_mtop_atomloop_all_init(sys);
while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
mass[i] = atom->m;
}
if (opts->seed == -1) {
opts->seed = make_seed();
fprintf(stderr,"Setting gen_seed to %d\n",opts->seed);
}
maxwell_speed(opts->tempi,opts->seed,sys,state->v);
stop_cm(stdout,state->natoms,mass,state->x,state->v);
sfree(mass);
}
*nmi = nrmols;
*mi = molinfo;
}
