int gmx_bond(int argc,char *argv[])
{
static char *desc[] = {
"g_bond makes a distribution of bond lengths. If all is well a",
"gaussian distribution should be made when using a harmonic potential.",
"bonds are read from a single group in the index file in order i1-j1",
"i2-j2 thru in-jn.[PAR]",
"[TT]-tol[tt] gives the half-width of the distribution as a fraction",
"of the bondlength ([TT]-blen[tt]). That means, for a bond of 0.2",
"a tol of 0.1 gives a distribution from 0.18 to 0.22.[PAR]",
"Option [TT]-d[tt] plots all the distances as a function of time.",
"This requires a structure file for the atom and residue names in",
"the output. If however the option [TT]-averdist[tt] is given (as well",
"or separately) the average bond length is plotted instead."
};
static char *bugs[] = {
"It should be possible to get bond information from the topology."
};
static real blen=-1.0,tol=0.1;
static bool bAver=TRUE,bAverDist=TRUE;
t_pargs pa[] = {
{ "-blen", FALSE, etREAL, {&blen},
"Bond length. By default length of first bond" },
{ "-tol", FALSE, etREAL, {&tol},
"Half width of distribution as fraction of blen" },
{ "-aver", FALSE, etBOOL, {&bAver},
"Average bond length distributions" },
{ "-averdist", FALSE, etBOOL, {&bAverDist},
"Average distances (turns on -d)" }
};
FILE *fp;
char *grpname,*fdist;
int gnx;
atom_id *index;
char title[STRLEN];
t_topology top;
int ePBC=-1;
rvec *x;
matrix box;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "bonds", ffWRITE },
{ efLOG, NULL, "bonds", ffOPTWR },
{ efXVG, "-d", "distance", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE ,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
if (bAverDist)
fdist = opt2fn("-d",NFILE,fnm);
else {
fdist = opt2fn_null("-d",NFILE,fnm);
if (fdist)
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x,NULL,box,
FALSE);
}
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
if ( !even(gnx) )
fprintf(stderr,"WARNING: odd number of atoms (%d) in group!\n",gnx);
fprintf(stderr,"Will gather information on %d bonds\n",gnx/2);
if (!bAver)
fp = ftp2FILE(efLOG,NFILE,fnm,"w");
else
fp = NULL;
do_bonds(fp,ftp2fn(efTRX,NFILE,fnm),opt2fn("-o",NFILE,fnm),fdist,gnx,index,
blen,tol,bAver,&top,ePBC,bAverDist);
do_view(opt2fn("-o",NFILE,fnm),"-nxy");
do_view(opt2fn_null("-d",NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
int main()
{
char coordinate_input[BUFSIZ];
char ammp_output[BUFSIZ];
char dictionary[BUFSIZ];
char work[1000],keep[1000];
char atype[20],aname[20];
char *fgets();
float sigma,emin;
int ifile,i,imreading,ii,myres;
FILE *in1,*dict,*output,*fopen();
printf(" atom definition file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
dictionary[ifile -i ] = work[ifile];
dictionary[ifile -i +1 ] = '\0';
}
/* now read in the atoms */
dict = fopen( dictionary, "r");
if( dict == NULL)
{ fprintf(stderr," sorry i can't open %s\n",dictionary); exit(0);}
inkinds = 0;
while ( fgets( work,256, dict) != NULL)
{
sscanf( work,"%s %f %f %f %f %f %f %f %f %f %f %f %f %f \n",
&kinds[inkinds].type[0],
&kinds[inkinds].r ,
&kinds[inkinds].theta ,
&sigma ,
&emin ,
&kinds[inkinds].Z ,
&kinds[inkinds].angle_inc,
&kinds[inkinds].X ,
&kinds[inkinds].jaa ,
&kinds[inkinds].mass ,
&kinds[inkinds].charge ,
&kinds[inkinds].V, &kinds[inkinds].U ,
&kinds[inkinds].hybrid
);
/* kinds[inkinds].theta *= 3.14159265/180.;
*/
sigma = sigma*sigma;
sigma = sigma*sigma*sigma;
/* kinds[inkinds].b = sqrt( 4.*emin*sigma*sigma);
kinds[inkinds].a = sqrt( 4.*emin*sigma);
*/
kinds[inkinds].b = sqrt( emin*sigma*sigma);
kinds[inkinds].a = sqrt( 2*emin*sigma);
inkinds ++;
if( inkinds > MAX_ATOM)
{ fprintf( stderr," too many kinds of atoms in dictionary\n");
exit(0); }
}
fclose( dict);
printf(" Residue dictionary directory:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
dictionary[ifile -i ] = work[ifile];
dictionary[ifile -i +1 ] = '\0';
}
ifile = ifile -i ;
if( ifile == 0 ){ dictionary[ifile++] = '.';
dictionary[ifile] = '\0'; }
if( dictionary[ifile-1] != '/')
{ ifile++; dictionary[ifile-1] = '/'; dictionary[ifile] = '\0';}
printf(" atom input coordinate file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
coordinate_input[ifile -i ] = work[ifile];
coordinate_input[ifile -i +1 ] = '\0';
}
printf(" AMMP file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
ammp_output[ifile -i ] = work[ifile];
ammp_output[ifile -i +1 ] = '\0';
}
in1 = fopen( coordinate_input, "r");
output = fopen( ammp_output, "w");
if (in1 == NULL) goto NO_IN1_FILE;
/* read in the first residue
* stuff is read into work when the residue number changes then
* work is copied into keep, so the first atom of any residue is
* going to be in the keep buffer. to initialize we read the
* first atom into keep
*/
keep[0] = '\0';
while( !(keep[0] == 'A' && keep[1] == 'T' && keep[2] == 'O' && keep[3] == 'M')
&& !(keep[0] == 'H'&& keep[1] == 'E'
&& keep[1] == 'T'&& keep[1] == 'A'&& keep[1] == 'T' ) )
{ if( fgets(keep,90,in1) == NULL) {
fprintf(stderr," no atoms in input file ? \n") ;
NO_IN1_FILE:
printf(" enter the dictionary name >\n");
fgets( keep, 90, stdin);
i=0; while( (keep[i] == ' ' || keep[i] == '\t') && keep[i] != '\0') i++;
for( imreading = 0; imreading < 3; imreading++)
{ aname[imreading] = toupper( keep[i + imreading] ); }
aname[3] = '\0';
goto NO_ATOMS;
}
}
imreading = 0;
while( imreading == 0)
{/* begining of imreading loop */
inres = 0;
for(i=0; i< MAX_RES; i++)
{ mykind[i] = -1;
defined[i] = -1;
name[i][0] = '\0';
x[i] = 0.;
y[i] = 0.;
z[i] = 0.;
}
sscanf( &keep[22],"%d",&myres);
sscanf(&keep[29],"%f %f %f",&x[inres],&y[inres],&z[inres]);
sscanf(&keep[11],"%s",&atype[0]);
sscanf(&keep[17],"%s",&aname[0]);
serial[inres] = 100*myres + inres;
ii = 0;
for( i=0; i< 3; i++ )
{
if( aname[i] == '\0') break;
name[inres][ii++] = (char)tolower(aname[i]);
}
name[inres][ii++] = '.';
for(i=0; i< 4; i++)
{
if( atype[i] == '\0' ) break;
name[inres][ii++] = (char)tolower(atype[i]);
}
name[inres][ii] = '\0';
a[inres] = 0.; b[inres] = 0.; q[inres] = 0.; mass[inres] = 1.;
defined[inres] = 0;
for( inres = 1; inres < MAX_RES; inres ++)
{ /* start of reading an atom loop */
if( fgets( work,90,in1) == NULL) {
imreading = 1; break; }
if( work[0] != 'A' && work[0] != 'H') {
imreading = 1; break; }
/*
printf("%s\n",work);
printf("%d\n",inres);
*/
sscanf( &work[22],"%d",&ii);
if( ii != myres )
{ii = 0; while( work[ii] != '\0'){ keep[ii] = work[ii] ; ii++;}
/* inres += 1; */
break;
}
sscanf(&work[29],"%f %f %f",&x[inres],&y[inres],&z[inres]);
sscanf(&work[11],"%s",&atype[0]);
sscanf(&work[17],"%s",&aname[0]);
serial[inres] = 100*myres + inres;
ii = 0;
for( i=0; i< 3; i++ )
{
if( aname[i] == '\0') break;
name[inres][ii++] = (char)tolower(aname[i]);
}
name[inres][ii++] = '.';
for(i=0; i< 4; i++)
{
if( atype[i] == '\0' ) break;
name[inres][ii++] = (char)tolower(atype[i]);
}
name[inres][ii] = '\0';
a[inres] = 0.; b[inres] = 0.; q[inres] = 0.; mass[inres] = 1.;
defined[inres] = 0;
}/* end of reading an atom loop */
/*
for( i=0; i< inres; i++)
printf(">%s<\n",&name[i][0]);
*/
/* if here then all of the atoms in the residue are read in */
/* now we have to open and read the dictionary file
* there could be atoms in either the residue or dictionary which
* are not there i.e. oxt for a residue or a missing H */
/* prepare the filename */
NO_ATOMS:
i = 0;
while(dictionary[i] != '\0') { work[i] = dictionary[i]; i++;}
ii = 0;
while(aname[ii] != '\0') {work[i] = aname[ii]; i++; ii++;}
work[i++] = '\0';
dict = fopen(work,"r");
if( dict == NULL ){
fprintf(stderr," dictionary %s not found \n", work);
write_atoms(output);
goto DONE;
}
/* read the number of atoms */
if(fgets( work,80,dict)==NULL)
{ fprintf(stderr,"BAD DICTIONARY %s\n",aname); exit(0);}
sscanf(work,"%d",&natoms);
read_atoms( dict,natoms );
write_atoms(output);
if(fgets( work,80,dict)==NULL)
{ fprintf(stderr,"BAD DICTIONARY %s\n",aname); exit(0);}
sscanf(work,"%d",&nbond);
do_bonds( dict,nbond,output);
inbondlist = nbond;
nangle = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&nangle);
do_angle(dict,nangle,output);
nhybrid = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&nhybrid);
do_hybrid(dict,nhybrid,output);
ntorsion = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&ntorsion);
do_torsion(dict,ntorsion,output);
DONE:
fclose( dict );
}/* end of imreading loop */
}/* end of module main */
int main (int argc, char *argv[]) {
static char usage[] = {
"Calculate positions of pseudo-atoms in a model for a transmembrane channel and\n"
"write output to FILE or pore.pdb and pore.itp.\n\n"
" -h\t\t show help\n"
" -v\t\t be verbose (= -debuglevel 30 )\n"
" -debug <NUM>\t set debuglevel (0..100)\n"
" -spec <NUM>\t default species id\n"
" -showspec\t show hard coded species\n\n"
" -o FILE\t pdb coordinate file\n"
" -s FILE\t itp topology file\n"
"\n"
" -f <file>\t read pore description from file (see below)\n"
" -R <r>\t Outer radius of the model\n"
" -P <r> <l>\t Pore region: inner radius and length\n"
" -M <r> <l>\t Mouth region: largest inner radius and length\n"
" -b dmin dmax g_min g_max (repeatable)\n"
"\t\tform bonds with angle gamma when atoms are no further apart\n"
"\t\tthan dmax Ang and g_min <= gamma <= g_max, g from [0°..90°] )\n"
" -c\t\t only write connectivity to output, no bond length or kB, kA\n"
" -x\t\t neither connectivity nor bond length to output (isolated atoms)\n"
" -kB <c>\t Force constant of bonds, in kJ mol^-1 nm^-2\n"
" -kA <c>\t Force constant of angles, in kJ mol^-1 rad^-2\n"
" -cc\t\t Center ccordinates on cavitybox, not on unitcell\n"
"\n"
"Pore volume calculation (setting any of these switches on profile calculation):\n"
"In order to enable volume calculation, set -volume explicitly!\n"
"ATTENTION: all these LENGTHs are in NANO METRE not Angstrom !\n"
" -profile [<file>] calculate the profile in addition to the volume\n"
" -z1, -z2 <z> profile between z1 and z2\n"
" -Rmax <r> integrate out to Rmax (also use for the total volume\n"
" integration if -profile is set)\n"
" -npoints <N> number of points per dimension in the integrals\n"
" -T temp Temperature in Kelvin [300]\n"
" -wca If set, only use the repulsive part of the Lennard-Jones\n"
" potential (split after Weeks, Chandler & Andersen [1971])\n"
" -plot xfarbe output of the potential in z slices\n"
" -nzplot number of plot slices \n"
"\nDescription of the input file:\n"
"------------------------------\n"
"Instead of using -R (RADIUS), -M (MOUTH), and -P (PORE) one can describe the system\n"
"in a more flexible manner with a geometry in put file. It can contain up to "
"MAXDOMAINS domains (i.e. MOUTH and PORE lines). Allowed lines:\n"
"# comment (skipped)\n"
"# RADIUS is the global outer radius (in Angstrom) of the cylinder\n"
"RADIUS r_outer\n"
"# domain type and radius at the upper and lower end of the domain;\n"
"# r_lower of domain i and r_upper of domain i+1 are typically identical\n"
"MOUTH r_upper r_lower length [species]\n"
"PORE r_upper r_lower length [species]\n"
};
int i, n_atoms, n_bonds, n_angles, n_bc;
int error;
real vol;
FILE *fp;
/*
segmentation fault if arrays to large
--->>
now that I have learned to calloc I should rewrite this
on purely aesthetical grounds !
<<----
*/
struct pdb_ATOM model[TOTALSITES];
struct itp_bond bonds[MAXBONDS];
struct itp_angle angles[MAXANGLES];
struct geom geometry;
struct std_input in;
struct potpars potential = {
NULL,
TEMPERATURE,
NFREEDOM_SPC,
CSIX_OW_MTH, CTWELVE_OW_MTH, 0.0,
0, NULL, NULL,
N_GAUSSLEG
};
struct pprofile profile = {
"LJprofile.dat",
FALSE,
FALSE,
POT_PLOT_SLICES,
NULL,
NZPROF,
1.5,
-2,2,
NULL
};
/* argument processing */
/* *** no sanity checks *** */
n_atoms = 0; /* number of sites ('atoms') in the model */
n_bonds = 0; /* number of bonds */
n_angles = 0; /* number of angles between bonds */
n_bc = 0; /* number of constraint conditions for generating bonds */
if (argc < 2) {
printf("Running with default values.\n\nType %s -h for help.\n", argv[0]);
debuglevel = IMPORTANT;
};
/* initialize defaults */
in = default_input ();
potential.u1 = vljcyl; /* use the full Lennard-Jones potential in
the configurational volume calculations
by default */
profile.pp = &potential;
/* rudimentary opt-processing.. yarch */
for (i = 1; i < argc; i++)
{
if (!strcmp(argv[i], "-debug")) {
debuglevel = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-v")) {
debuglevel = VERBOSE;
} else if (!strcmp(argv[i], "-h")) {
print_usage(argv[0],usage);
exit(1);
} else if (!strcmp(argv[i], "-showspec")) {
print_species ();
exit(1);
} else if (!strcmp(argv[i], "-o")) {
in.coordfile = argv[++i];
} else if (!strcmp(argv[i], "-s")) {
in.topofile = argv[++i];
} else if (!strcmp(argv[i], "-f")) {
in.datafile = argv[++i];
} else if (!strcmp(argv[i], "-R")) {
in.r_outer = atof(argv[++i]);
} else if (!strcmp(argv[i], "-M")) {
in.r_mouth = atof(argv[++i]);
in.l_mouth = atof(argv[++i]);
} else if (!strcmp(argv[i], "-P")) {
in.r_pore = atof(argv[++i]);
in.l_pore = atof(argv[++i]);
} else if (!strcmp(argv[i], "-spec")) {
in.specid = atoi(argv[++i]);
} else if (!strcmp(argv[i], "-b")) {
if (n_bc > MAXBONDCONSTRAINTS) {
fatal_error (1,
"Error: too many bond constraints, maximum is %d.\n",
MAXBONDCONSTRAINTS);
}
in.bc[n_bc].serial = n_bc;
in.bc[n_bc].dmin = atof(argv[++i]);
in.bc[n_bc].dmax = atof(argv[++i]);
in.bc[n_bc].gamma_min = atof(argv[++i]);
in.bc[n_bc].gamma_max = atof(argv[++i]);
in.n_bc = ++n_bc;
} else if (!strcmp(argv[i], "-c")) {
in.connectonly = TRUE;
} else if (!strcmp(argv[i], "-x")) {
in.atomsonly = TRUE;
} else if (!strcmp(argv[i], "-cc")) {
in.shiftcbox = TRUE;
} else if (!strcmp(argv[i], "-kB")) {
in.k_bond = atof(argv[++i]);
} else if (!strcmp(argv[i], "-kA")) {
in.k_angle = atof(argv[++i]);
} else if (!strcmp(argv[i], "-volume")) {
profile.bSet = TRUE;
} else if (!strcmp(argv[i], "-z1")) {
profile.bSet = TRUE;
profile.z1 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-z2")) {
profile.bSet = TRUE;
profile.z2 = atof(argv[++i]);
} else if (!strcmp(argv[i], "-Rmax")) {
profile.bSet = TRUE;
profile.Rmax = atof(argv[++i]);
} else if (!strcmp(argv[i], "-profile")) {
profile.bSet = TRUE;
if (i < argc-1 && argv[i+1][0] != '-')
strncpy(profile.fn,argv[++i],STRLEN);
} else if (!strcmp(argv[i], "-npoints")) {
potential.ngaussleg = atof(argv[++i]);
} else if (!strcmp(argv[i], "-T")) {
potential.Temp = atof(argv[++i]);
} else if (!strcmp(argv[i], "-wca")) {
potential.u1 = vRljcyl;
} else if (!strcmp(argv[i], "-plot")) {
profile.bPlot = TRUE;
} else if (!strcmp(argv[i], "-nzplot")) {
profile.bPlot = TRUE;
profile.nzplot = atoi(argv[++i]);
} else {
mesg(OFF,"Unknown option: %s",argv[i]);
};
};
mesg (ALL, "TOTALSITES %d\n", TOTALSITES);
mesg (ALL,
"MAXBONDS %d\nsizeof struct bond %d, sizeof bonds[] %d\n",
MAXBONDS, sizeof (struct itp_bond), sizeof (bonds));
mesg (ALL,
"MAXANGLES %d\nsizeof struct angle %d, sizeof angles[] %d\n",
MAXANGLES, sizeof (struct itp_angle), sizeof (angles));
error = input_geom (&in, &geometry);
setup_domain (&geometry);
unitcell (&geometry);
cavitybox (&geometry);
n_atoms = do_coordinates (model, &geometry);
if (!geometry.atomsonly) {
n_bonds = do_bonds (bonds, model, &geometry);
n_angles = do_angles (angles, bonds, &geometry);
} else {
n_bonds = n_angles = 0;
}
print_geom (&geometry);
mesg (WARN, "\nNumber of sites: %d", n_atoms);
if (!geometry.atomsonly) {
mesg (WARN,
"Number of bonds: %d within max cut-off %5.2f Ang (no double-counting)",
n_bonds, find_dmax (geometry.bc, geometry.nbc));
mesg (WARN, "Number of angles: %d (no double-counting)\n", n_angles);
}
center (model, &geometry);
error = write_topology (model, bonds, angles, &geometry);
error = write_pdb (model, bonds, &geometry);
/*
calculate pore volume, based on J. S. Rowlinson, J Chem Soc,
Faraday Trans. 2, 82 (1986), 1801, (which didnt really work), and
discussion with Andrew Horsefield. */
if (profile.bSet) {
vol = volume(&potential,model,geometry.domain[1],&profile);
/* pore profile (already calculated in volume ) */
fp=fopen(profile.fn,"w");
if (fp) {
for(i=0;i<NZPROF;i++) {
fprintf(fp,"%f %f\n",profile.r[i][0],profile.r[i][1]);
}
fclose(fp);
}
free(profile.r);
}
return error < 0 ? 1 : 0;
};
