void read_atoms_neb(str255 infilename)
{
str255 fname;
int i, k, n;
/* keep a copy of the outfile name without replica suffix */
neb_outfilename = strdup(outfilename);
/* read positions of initial configuration */
if (0==myrank) {
sprintf(fname, "%s.%02d", infilename, 0);
myrank = 1; /* avoid double info messages */
read_atoms(fname);
myrank = 0;
alloc_pos();
/* compute and write energy of initial configuration */
calc_forces(0);
neb_image_energies[0]=tot_pot_energy;
sprintf(outfilename, "%s.%02d", neb_outfilename, 0);
write_eng_file_header();
write_eng_file(0);
fclose(eng_file);
eng_file = NULL;
}
/* read positions of final configuration */
else if (neb_nrep-1==myrank) {
sprintf(fname, "%s.%02d", infilename, neb_nrep-1);
read_atoms(fname);
if (NULL==pos) alloc_pos();
/* compute and write energy of initial configuration */
calc_forces(0);
neb_image_energies[ neb_nrep-1]=tot_pot_energy;
sprintf(outfilename, "%s.%02d", neb_outfilename, neb_nrep-1);
write_eng_file_header();
write_eng_file(0);
fclose(eng_file);
eng_file = NULL;
}
else
{
/* read positions of my configuration */
sprintf(fname, "%s.%02d", infilename, myrank);
printf("rank: %d reading %s.%02d\n",myrank, infilename, myrank);fflush(stdout);
read_atoms(fname);
if (NULL==pos) alloc_pos();
sprintf(outfilename, "%s.%02d", neb_outfilename, myrank);
}
}
int main(int argc, char **argv)
{
int tablesize;
int n,i,j,k,l;
/* Read command line arguments */
read_command_line(argc,argv);
/* Read Parameters from parameter file */
read_parameters();
tablesize = slots*ntypes*ntypes*ntypes*ntypes*sizeof(real);
histogram = (real *) malloc(tablesize);
if (NULL==histogram) error("Cannot allocate memory for histograms.");
hist_dim.n = slots;
hist_dim.i = ntypes;
hist_dim.j = ntypes;
hist_dim.k = ntypes;
hist_dim.l = ntypes;
for (n=0; n<slots; ++n)
for (i=0; i<ntypes; ++i)
for (j=0; j<ntypes; ++j)
for (k=0; k<ntypes; ++k)
for (l=0; l<ntypes; ++l)
*PTR_5D_V(histogram,n,i,j,k,l,hist_dim) = 0.0;
r2_cut = SQR(r_max);
/* read box from file header */
if (box_from_header) read_box(infilename);
/* Initialize cell data structures */
init_cells();
/* Read atoms */
read_atoms(infilename);
/* Calculate the torsion angles */
calc_angles();
/* Output results */
write_data();
return 0;
}
static struct classifier_config*
read_config(FILE *input)
{
assert(input);
struct file_range types_section, atoms_section;
struct classifier_config *config = NULL;
struct classifier_types *types = NULL;
if (!(types = classifier_types_new()) ||
!(config = classifier_config_new()) ||
check_file(input, &types_section, &atoms_section) ||
read_types(types, input, types_section) ||
read_atoms(config, types, input, atoms_section) ||
config_copy_classes(config, types)) {
classifier_config_free(config);
config = NULL;
}
classifier_types_free(types);
return config;
}
int main(int argc, char **argv)
{
/* Read command line arguments */
read_command_line(argc,argv);
/* Read Parameters from parameter file */
read_parameters();
/* read box from file header */
if (box_from_header) read_box(infilename);
#ifdef TERSOFF
/* Compute Tersoff parameters */
init_tersoff();
#endif
/* Initialize cell data structures */
init_cells();
/* Read atoms */
read_atoms(infilename);
/* Compute neighbour tables */
do_work(do_neighbour_tables);
first = 0;
do_work(do_neighbour_tables);
/* Search for rings */
search_rings();
/* Output ring statistics */
write_data();
return 0;
}
void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
gpp_atomtype_t atype, t_symtab *tab,
gmx_bool bAllowOverrideRTP)
{
FILE *in;
char filebase[STRLEN], line[STRLEN], header[STRLEN];
int i, nrtp, maxrtp, bt, nparam;
int dum1, dum2, dum3;
t_restp *rrtp, *header_settings;
gmx_bool bNextResidue, bError;
int firstrtp;
fflib_filename_base(rrdb, filebase, STRLEN);
in = fflib_open(rrdb);
if (debug)
{
fprintf(debug, "%9s %5s", "Residue", "atoms");
for (i = 0; i < ebtsNR; i++)
{
fprintf(debug, " %10s", btsNames[i]);
}
fprintf(debug, "\n");
}
snew(header_settings, 1);
/* these bonded parameters will overwritten be when *
* there is a [ bondedtypes ] entry in the .rtp file */
header_settings->rb[ebtsBONDS].type = 1; /* normal bonds */
header_settings->rb[ebtsANGLES].type = 1; /* normal angles */
header_settings->rb[ebtsPDIHS].type = 1; /* normal dihedrals */
header_settings->rb[ebtsIDIHS].type = 2; /* normal impropers */
header_settings->rb[ebtsEXCLS].type = 1; /* normal exclusions */
header_settings->rb[ebtsCMAP].type = 1; /* normal cmap torsions */
header_settings->bKeepAllGeneratedDihedrals = FALSE;
header_settings->nrexcl = 3;
header_settings->bGenerateHH14Interactions = TRUE;
header_settings->bRemoveDihedralIfWithImproper = TRUE;
/* Column 5 & 6 aren't really bonded types, but we include
* them here to avoid introducing a new section:
* Column 5 : This controls the generation of dihedrals from the bonding.
* All possible dihedrals are generated automatically. A value of
* 1 here means that all these are retained. A value of
* 0 here requires generated dihedrals be removed if
* * there are any dihedrals on the same central atoms
* specified in the residue topology, or
* * there are other identical generated dihedrals
* sharing the same central atoms, or
* * there are other generated dihedrals sharing the
* same central bond that have fewer hydrogen atoms
* Column 6: Number of bonded neighbors to exclude.
* Column 7: Generate 1,4 interactions between two hydrogen atoms
* Column 8: Remove proper dihedrals if centered on the same bond
* as an improper dihedral
*/
get_a_line(in, line, STRLEN);
if (!get_header(line, header))
{
gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
}
if (gmx_strncasecmp("bondedtypes", header, 5) == 0)
{
get_a_line(in, line, STRLEN);
if ((nparam = sscanf(line, "%d %d %d %d %d %d %d %d",
&header_settings->rb[ebtsBONDS].type, &header_settings->rb[ebtsANGLES].type,
&header_settings->rb[ebtsPDIHS].type, &header_settings->rb[ebtsIDIHS].type,
&dum1, &header_settings->nrexcl, &dum2, &dum3)) < 4)
{
gmx_fatal(FARGS, "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n", rrdb, line);
}
header_settings->bKeepAllGeneratedDihedrals = (dum1 != 0);
header_settings->bGenerateHH14Interactions = (dum2 != 0);
header_settings->bRemoveDihedralIfWithImproper = (dum3 != 0);
get_a_line(in, line, STRLEN);
if (nparam < 5)
{
fprintf(stderr, "Using default: not generating all possible dihedrals\n");
header_settings->bKeepAllGeneratedDihedrals = FALSE;
}
if (nparam < 6)
{
fprintf(stderr, "Using default: excluding 3 bonded neighbors\n");
header_settings->nrexcl = 3;
}
if (nparam < 7)
{
fprintf(stderr, "Using default: generating 1,4 H--H interactions\n");
header_settings->bGenerateHH14Interactions = TRUE;
}
if (nparam < 8)
{
fprintf(stderr, "Using default: removing proper dihedrals found on the same bond as a proper dihedral\n");
header_settings->bRemoveDihedralIfWithImproper = TRUE;
}
}
else
{
fprintf(stderr,
"Reading .rtp file without '[ bondedtypes ]' directive,\n"
"Will proceed as if the entry was:\n");
print_resall_header(stderr, header_settings);
}
/* We don't know the current size of rrtp, but simply realloc immediately */
nrtp = *nrtpptr;
rrtp = *rtp;
maxrtp = nrtp;
while (!feof(in))
{
if (nrtp >= maxrtp)
{
maxrtp += 100;
srenew(rrtp, maxrtp);
}
/* Initialise rtp entry structure */
rrtp[nrtp] = *header_settings;
if (!get_header(line, header))
{
gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
}
rrtp[nrtp].resname = gmx_strdup(header);
rrtp[nrtp].filebase = gmx_strdup(filebase);
get_a_line(in, line, STRLEN);
bError = FALSE;
bNextResidue = FALSE;
do
{
if (!get_header(line, header))
{
bError = TRUE;
}
else
{
bt = get_bt(header);
if (bt != NOTSET)
{
/* header is an bonded directive */
bError = !read_bondeds(bt, in, line, &rrtp[nrtp]);
}
else if (gmx_strncasecmp("atoms", header, 5) == 0)
{
/* header is the atoms directive */
bError = !read_atoms(in, line, &(rrtp[nrtp]), tab, atype);
}
else
{
/* else header must be a residue name */
bNextResidue = TRUE;
}
}
if (bError)
{
gmx_fatal(FARGS, "in .rtp file in residue %s at line:\n%s\n",
rrtp[nrtp].resname, line);
}
}
while (!feof(in) && !bNextResidue);
if (rrtp[nrtp].natom == 0)
{
gmx_fatal(FARGS, "No atoms found in .rtp file in residue %s\n",
rrtp[nrtp].resname);
}
if (debug)
{
fprintf(debug, "%3d %5s %5d",
nrtp+1, rrtp[nrtp].resname, rrtp[nrtp].natom);
for (i = 0; i < ebtsNR; i++)
{
fprintf(debug, " %10d", rrtp[nrtp].rb[i].nb);
}
fprintf(debug, "\n");
}
firstrtp = -1;
for (i = 0; i < nrtp; i++)
{
if (gmx_strcasecmp(rrtp[i].resname, rrtp[nrtp].resname) == 0)
{
firstrtp = i;
}
}
if (firstrtp == -1)
{
nrtp++;
fprintf(stderr, "\rResidue %d", nrtp);
fflush(stderr);
}
else
{
if (firstrtp >= *nrtpptr)
{
gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'",
rrtp[nrtp].resname, rrdb);
}
if (bAllowOverrideRTP)
{
fprintf(stderr, "\n");
fprintf(stderr, "Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
rrtp[nrtp].resname, rrdb, rrtp[firstrtp].filebase);
/* We should free all the data for this entry.
* The current code gives a lot of dangling pointers.
*/
clear_t_restp(&rrtp[nrtp]);
}
else
{
gmx_fatal(FARGS, "Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.", rrtp[nrtp].resname, rrtp[firstrtp].filebase, rrdb);
}
}
}
gmx_ffclose(in);
/* give back unused memory */
srenew(rrtp, nrtp);
fprintf(stderr, "\nSorting it all out...\n");
qsort(rrtp, nrtp, (size_t)sizeof(rrtp[0]), comprtp);
check_rtp(nrtp, rrtp, rrdb);
*nrtpptr = nrtp;
*rtp = rrtp;
}
void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
gpp_atomtype_t atype, t_symtab *tab,
gmx_bool bAllowOverrideRTP)
{
FILE *in;
char filebase[STRLEN],*ptr,line[STRLEN],header[STRLEN];
int i,nrtp,maxrtp,bt,nparam;
int dum1,dum2,dum3;
t_restp *rrtp;
gmx_bool bNextResidue,bError;
int bts[ebtsNR];
gmx_bool bAlldih;
int nrexcl;
gmx_bool HH14;
gmx_bool bRemoveDih;
int firstrtp;
fflib_filename_base(rrdb,filebase,STRLEN);
in = fflib_open(rrdb);
if (debug) {
fprintf(debug,"%9s %5s", "Residue", "atoms");
for(i=0; i<ebtsNR; i++)
fprintf(debug," %10s",btsNames[i]);
fprintf(debug,"\n");
}
/* these bonded parameters will overwritten be when *
* there is a [ bondedtypes ] entry in the .rtp file */
bts[ebtsBONDS] = 1; /* normal bonds */
bts[ebtsANGLES] = 1; /* normal angles */
bts[ebtsPDIHS] = 1; /* normal dihedrals */
bts[ebtsIDIHS] = 2; /* normal impropers */
bts[ebtsEXCLS] = 1; /* normal exclusions */
bts[ebtsCMAP] = 1; /* normal cmap torsions */
bAlldih = FALSE;
nrexcl = 3;
HH14 = TRUE;
bRemoveDih = TRUE;
/* Column 5 & 6 aren't really bonded types, but we include
* them here to avoid introducing a new section:
* Column 5: 1 means generate all dihedrals, 0 not.
* Column 6: Number of bonded neighbors to exclude.
* Coulmn 7: Generate 1,4 interactions between pairs of hydrogens
* Column 8: Remove impropers over the same bond as a proper dihedral
*/
get_a_line(in,line,STRLEN);
if (!get_header(line,header))
gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
if (gmx_strncasecmp("bondedtypes",header,5)==0) {
get_a_line(in,line,STRLEN);
if ((nparam=sscanf(line,"%d %d %d %d %d %d %d %d",
&bts[ebtsBONDS],&bts[ebtsANGLES],
&bts[ebtsPDIHS],&bts[ebtsIDIHS],
&dum1,&nrexcl,&dum2,&dum3)) < 4 )
{
gmx_fatal(FARGS,"need at least 4 (up to 8) parameters in .rtp file at line:\n%s\n",line);
}
bAlldih = (dum1 != 0);
HH14 = (dum2 != 0);
bRemoveDih = (dum3 != 0);
get_a_line(in,line,STRLEN);
if(nparam<5) {
fprintf(stderr,"Using default: not generating all possible dihedrals\n");
bAlldih = FALSE;
}
if(nparam<6) {
fprintf(stderr,"Using default: excluding 3 bonded neighbors\n");
nrexcl = 3;
}
if(nparam<7) {
fprintf(stderr,"Using default: generating 1,4 H--H interactions\n");
HH14 = TRUE;
}
if(nparam<8) {
fprintf(stderr,"Using default: removing impropers on same bond as a proper\n");
bRemoveDih = TRUE;
}
} else {
fprintf(stderr,
"Reading .rtp file without '[ bondedtypes ]' directive,\n"
"Will proceed as if the entry\n"
"\n"
"\n[ bondedtypes ]"
"\n; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih"
"\n %3d %3d %3d %3d %3d %3d %3d %3d"
"\n"
"was present at the beginning of %s",
bts[0],bts[1],bts[2],bts[3], bAlldih ? 1 : 0,nrexcl,HH14,bRemoveDih,rrdb);
}
/* We don't know the current size of rrtp, but simply realloc immediately */
nrtp = *nrtpptr;
rrtp = *rtp;
maxrtp = nrtp;
while (!feof(in)) {
if (nrtp >= maxrtp) {
maxrtp+=100;
srenew(rrtp,maxrtp);
}
clear_t_restp(&rrtp[nrtp]);
if (!get_header(line,header))
gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
rrtp[nrtp].resname = strdup(header);
rrtp[nrtp].filebase = strdup(filebase);
/* Set the bonded types */
rrtp[nrtp].bAlldih = bAlldih;
rrtp[nrtp].nrexcl = nrexcl;
rrtp[nrtp].HH14 = HH14;
rrtp[nrtp].bRemoveDih = bRemoveDih;
for(i=0; i<ebtsNR; i++) {
rrtp[nrtp].rb[i].type = bts[i];
}
get_a_line(in,line,STRLEN);
bError=FALSE;
bNextResidue=FALSE;
do {
if (!get_header(line,header)) {
bError = TRUE;
} else {
bt = get_bt(header);
if (bt != NOTSET) {
/* header is an bonded directive */
bError = !read_bondeds(bt,in,line,&rrtp[nrtp]);
} else if (gmx_strncasecmp("atoms",header,5) == 0) {
/* header is the atoms directive */
bError = !read_atoms(in,line,&(rrtp[nrtp]),tab,atype);
} else {
/* else header must be a residue name */
bNextResidue = TRUE;
}
}
if (bError)
gmx_fatal(FARGS,"in .rtp file in residue %s at line:\n%s\n",
rrtp[nrtp].resname,line);
} while (!feof(in) && !bNextResidue);
if (rrtp[nrtp].natom == 0)
gmx_fatal(FARGS,"No atoms found in .rtp file in residue %s\n",
rrtp[nrtp].resname);
if (debug) {
fprintf(debug,"%3d %5s %5d",
nrtp+1,rrtp[nrtp].resname,rrtp[nrtp].natom);
for(i=0; i<ebtsNR; i++)
fprintf(debug," %10d",rrtp[nrtp].rb[i].nb);
fprintf(debug,"\n");
}
firstrtp = -1;
for(i=0; i<nrtp; i++) {
if (gmx_strcasecmp(rrtp[i].resname,rrtp[nrtp].resname) == 0) {
firstrtp = i;
}
}
if (firstrtp == -1) {
nrtp++;
fprintf(stderr,"\rResidue %d",nrtp);
} else {
if (firstrtp >= *nrtpptr)
{
gmx_fatal(FARGS,"Found a second entry for '%s' in '%s'",
rrtp[nrtp].resname,rrdb);
}
if (bAllowOverrideRTP)
{
fprintf(stderr,"\n");
fprintf(stderr,"Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
rrtp[nrtp].resname,rrdb,rrtp[firstrtp].filebase);
/* We should free all the data for this entry.
* The current code gives a lot of dangling pointers.
*/
clear_t_restp(&rrtp[nrtp]);
}
else
{
gmx_fatal(FARGS,"Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.",rrtp[nrtp].resname,rrtp[firstrtp].filebase,rrdb);
}
}
}
ffclose(in);
/* give back unused memory */
srenew(rrtp,nrtp);
fprintf(stderr,"\nSorting it all out...\n");
qsort(rrtp,nrtp,(size_t)sizeof(rrtp[0]),comprtp);
check_rtp(nrtp,rrtp,rrdb);
*nrtpptr = nrtp;
*rtp = rrtp;
}
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 */
/*
* md_initialize: Initializes MD module: loads initial atoms positions,
* velocities, setups parameters of potentials.
* Parameters:
* cls_file - file in CLSMAN format (initial positions,
* velocities, atom species)
* input_file - file with modelling parameters
*/
void md_initialize(const char *cls_file, const char *input_file)
{
read_atoms(cls_file);
read_inputfile(input_file);
}
