1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
23 * bugs must be traceable. We will be happy to consider code for
24 * inclusion in the official distribution, but derived work must not
25 * be called official GROMACS. Details are found in the README & COPYING
26 * files - if they are missing, get the official version at www.gromacs.org.
28 * To help us fund GROMACS development, we humbly ask that you cite
29 * the papers on the package - you can find them in the top README file.
31 * For more info, check our website at http://www.gromacs.org
34 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
51 #include "gmx_fatal.h"
53 #include "gpp_nextnb.h"
66 #include "gen_vsite.h"
69 #include "fflibutil.h"
72 /* this must correspond to enum in pdb2top.h */
73 const char *hh[ehisNR] = { "HISD", "HISE", "HISH", "HIS1" };
75 static int missing_atoms(t_restp *rp, int resind,t_atoms *at, int i0, int i)
79 gmx_bool bFound, bRet;
82 for (j=0; j<rp->natom; j++)
84 name=*(rp->atomname[j]);
88 bFound = (bFound || !gmx_strcasecmp(*(at->atomname[k]),name));
93 fprintf(stderr,"\nWARNING: "
94 "atom %s is missing in residue %s %d in the pdb file\n",
95 name,*(at->resinfo[resind].name),at->resinfo[resind].nr);
96 if (name[0]=='H' || name[0]=='h')
98 fprintf(stderr," You might need to add atom %s to the hydrogen database of building block %s\n"
99 " in the file %s.hdb (see the manual)\n",
100 name,*(at->resinfo[resind].rtp),rp->filebase);
102 fprintf(stderr,"\n");
109 gmx_bool is_int(double x)
111 const double tol = 1e-4;
118 return (fabs(x-ix) < tol);
121 static void swap_strings(char **s,int i,int j)
131 choose_ff(const char *ffsel,
132 char *forcefield, int ff_maxlen,
133 char *ffdir, int ffdir_maxlen)
136 char **ffdirs,**ffs,**ffs_dir,*ptr;
137 int i,j,sel,cwdsel,nfound;
138 char buf[STRLEN],**desc;
142 nff = fflib_search_file_in_dirend(fflib_forcefield_itp(),
143 fflib_forcefield_dir_ext(),
148 gmx_fatal(FARGS,"No force fields found (files with name '%s' in subdirectories ending on '%s')",
149 fflib_forcefield_itp(),fflib_forcefield_dir_ext());
152 /* Replace with unix path separators */
153 if(DIR_SEPARATOR!='/')
157 while( (ptr=strchr(ffdirs[i],DIR_SEPARATOR))!=NULL )
164 /* Store the force field names in ffs */
169 /* Remove the path from the ffdir name - use our unix standard here! */
170 ptr = strrchr(ffdirs[i],'/');
173 ffs[i] = strdup(ffdirs[i]);
174 ffs_dir[i] = low_gmxlibfn(ffdirs[i],FALSE,FALSE);
175 if (ffs_dir[i] == NULL)
177 gmx_fatal(FARGS,"Can no longer find file '%s'",ffdirs[i]);
182 ffs[i] = strdup(ptr+1);
183 ffs_dir[i] = strdup(ffdirs[i]);
185 ffs_dir[i][strlen(ffs_dir[i])-strlen(ffs[i])-1] = '\0';
186 /* Remove the extension from the ffdir name */
187 ffs[i][strlen(ffs[i])-strlen(fflib_forcefield_dir_ext())] = '\0';
197 if ( strcmp(ffs[i],ffsel)==0 )
199 /* Matching ff name */
203 if( strncmp(ffs_dir[i],".",1)==0 )
220 "Force field '%s' occurs in %d places. pdb2gmx is using the one in the\n"
221 "current directory. Use interactive selection (not the -ff option) if\n"
222 "you would prefer a different one.\n",ffsel,nfound);
227 "Force field '%s' occurs in %d places, but not in the current directory.\n"
228 "Run without the -ff switch and select the force field interactively.",ffsel,nfound);
233 gmx_fatal(FARGS,"Could not find force field '%s' in current directory, install tree or GMXDATA path.",ffsel);
239 for(i=0; (i<nff); i++)
241 sprintf(buf,"%s%c%s%s%c%s",
242 ffs_dir[i],DIR_SEPARATOR,
243 ffs[i],fflib_forcefield_dir_ext(),DIR_SEPARATOR,
244 fflib_forcefield_doc());
247 /* We don't use fflib_open, because we don't want printf's */
248 fp = ffopen(buf,"r");
249 snew(desc[i],STRLEN);
250 get_a_line(fp,desc[i],STRLEN);
255 desc[i] = strdup(ffs[i]);
258 /* Order force fields from the same dir alphabetically
259 * and put deprecated force fields at the end.
261 for(i=0; (i<nff); i++)
263 for(j=i+1; (j<nff); j++)
265 if (strcmp(ffs_dir[i],ffs_dir[j]) == 0 &&
266 ((desc[i][0] == '[' && desc[j][0] != '[') ||
267 ((desc[i][0] == '[' || desc[j][0] != '[') &&
268 gmx_strcasecmp(desc[i],desc[j]) > 0)))
270 swap_strings(ffdirs,i,j);
271 swap_strings(ffs ,i,j);
272 swap_strings(desc ,i,j);
277 printf("\nSelect the Force Field:\n");
278 for(i=0; (i<nff); i++)
280 if (i == 0 || strcmp(ffs_dir[i-1],ffs_dir[i]) != 0)
282 if( strcmp(ffs_dir[i],".")==0 )
284 printf("From current directory:\n");
288 printf("From '%s':\n",ffs_dir[i]);
291 printf("%2d: %s\n",i+1,desc[i]);
298 pret = fgets(buf,STRLEN,stdin);
302 sscanf(buf,"%d",&sel);
306 while ( pret==NULL || (sel < 0) || (sel >= nff));
308 /* Check for a current limitation of the fflib code.
309 * It will always read from the first ff directory in the list.
310 * This check assumes that the order of ffs matches the order
311 * in which fflib_open searches ff library files.
315 if (strcmp(ffs[i],ffs[sel]) == 0)
317 gmx_fatal(FARGS,"Can only select the first of multiple force field entries with directory name '%s%s' in the list. If you want to use the next entry, run pdb2gmx in a different directory or rename or move the force field directory present in the current working directory.",
318 ffs[sel],fflib_forcefield_dir_ext());
327 if (strlen(ffs[sel]) >= (size_t)ff_maxlen)
329 gmx_fatal(FARGS,"Length of force field name (%d) >= maxlen (%d)",
330 strlen(ffs[sel]),ff_maxlen);
332 strcpy(forcefield,ffs[sel]);
334 if (strlen(ffdirs[sel]) >= (size_t)ffdir_maxlen)
336 gmx_fatal(FARGS,"Length of force field dir (%d) >= maxlen (%d)",
337 strlen(ffdirs[sel]),ffdir_maxlen);
339 strcpy(ffdir,ffdirs[sel]);
341 for(i=0; (i<nff); i++)
352 void choose_watermodel(const char *wmsel,const char *ffdir,
355 const char *fn_watermodels="watermodels.dat";
356 char fn_list[STRLEN];
363 if (strcmp(wmsel,"none") == 0)
369 else if (strcmp(wmsel,"select") != 0)
371 *watermodel = strdup(wmsel);
376 sprintf(fn_list,"%s%c%s",ffdir,DIR_SEPARATOR,fn_watermodels);
378 if (!fflib_fexist(fn_list))
380 fprintf(stderr,"No file '%s' found, will not include a water model\n",
387 fp = fflib_open(fn_list);
388 printf("\nSelect the Water Model:\n");
391 while (get_a_line(fp,buf,STRLEN))
394 snew(model[nwm],STRLEN);
395 sscanf(buf,"%s%n",model[nwm],&i);
399 fprintf(stderr,"%2d: %s\n",nwm+1,buf+i);
408 fprintf(stderr,"%2d: %s\n",nwm+1,"None");
412 pret = fgets(buf,STRLEN,stdin);
416 sscanf(buf,"%d",&sel);
420 while (pret == NULL || sel < 0 || sel > nwm);
428 *watermodel = strdup(model[sel]);
438 static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
439 t_restp restp[], gmx_residuetype_t rt)
441 int i,j,prevresind,resind,i0,prevcg,cg,curcg;
443 gmx_bool bProt, bNterm;
460 for(i=0; (i<at->nr); i++) {
462 if (at->atom[i].resind != resind) {
463 resind = at->atom[i].resind;
464 bProt = gmx_residuetype_is_protein(rt,*(at->resinfo[resind].name));
465 bNterm=bProt && (resind == 0);
467 nmissat += missing_atoms(&restp[prevresind],prevresind,at,i0,i);
471 if (at->atom[i].m == 0) {
473 fprintf(debug,"atom %d%s: curcg=%d, prevcg=%d, cg=%d\n",
474 i+1,*(at->atomname[i]),curcg,prevcg,
475 j==NOTSET ? NOTSET : restp[resind].cgnr[j]);
478 name=*(at->atomname[i]);
479 j=search_jtype(&restp[resind],name,bNterm);
480 at->atom[i].type = restp[resind].atom[j].type;
481 at->atom[i].q = restp[resind].atom[j].q;
482 at->atom[i].m = get_atomtype_massA(restp[resind].atom[j].type,
484 cg = restp[resind].cgnr[j];
485 /* A charge group number -1 signals a separate charge group
488 if ( (cg == -1) || (cg != prevcg) || (resind != prevresind) ) {
493 fprintf(debug,"atom %d%s: curcg=%d, qt=%g, is_int=%d\n",
494 i+1,*(at->atomname[i]),curcg,qt,is_int(qt));
503 at->atom[i].typeB = at->atom[i].type;
504 at->atom[i].qB = at->atom[i].q;
505 at->atom[i].mB = at->atom[i].m;
507 nmissat += missing_atoms(&restp[resind],resind,at,i0,i);
512 static void print_top_heavy_H(FILE *out, real mHmult)
515 fprintf(out,"; Using deuterium instead of hydrogen\n\n");
516 else if (mHmult == 4.0)
517 fprintf(out,"#define HEAVY_H\n\n");
518 else if (mHmult != 1.0)
519 fprintf(stderr,"WARNING: unsupported proton mass multiplier (%g) "
520 "in pdb2top\n",mHmult);
523 void print_top_comment(FILE *out,
524 const char *filename,
525 const char *generator,
530 char ffdir_parent[STRLEN];
533 nice_header(out,filename);
534 fprintf(out,";\tThis is a %s topology file\n;\n",bITP ? "include" : "standalone");
535 fprintf(out,";\tIt was generated using program:\n;\t%s\n;\n",
536 (NULL == generator) ? "unknown" : generator);
537 fprintf(out,";\tCommand line was:\n;\t%s\n;\n",command_line());
539 if(strchr(ffdir,'/')==NULL)
541 fprintf(out,";\tForce field was read from the standard Gromacs share directory.\n;\n\n");
543 else if(ffdir[0]=='.')
545 fprintf(out,";\tForce field was read from current directory or a relative path - path added.\n;\n\n");
549 strncpy(ffdir_parent,ffdir,STRLEN-1);
550 ffdir_parent[STRLEN-1]='\0'; /*make sure it is 0-terminated even for long string*/
551 p=strrchr(ffdir_parent,'/');
556 ";\tForce field data was read from:\n"
560 ";\tThis might be a non-standard force field location. When you use this topology, the\n"
561 ";\tforce field must either be present in the current directory, or the location\n"
562 ";\tspecified in the GMXLIB path variable or with the 'include' mdp file option.\n;\n\n",
567 void print_top_header(FILE *out,const char *filename,
568 const char *title,gmx_bool bITP,const char *ffdir,real mHmult)
572 print_top_comment(out,filename,title,ffdir,bITP);
574 print_top_heavy_H(out, mHmult);
575 fprintf(out,"; Include forcefield parameters\n");
577 p=strrchr(ffdir,'/');
578 p = (ffdir[0]=='.' || p==NULL) ? ffdir : p+1;
580 fprintf(out,"#include \"%s/%s\"\n\n",p,fflib_forcefield_itp());
583 static void print_top_posre(FILE *out,const char *pr)
585 fprintf(out,"; Include Position restraint file\n");
586 fprintf(out,"#ifdef POSRES\n");
587 fprintf(out,"#include \"%s\"\n",pr);
588 fprintf(out,"#endif\n\n");
591 static void print_top_water(FILE *out,const char *ffdir,const char *water)
596 fprintf(out,"; Include water topology\n");
598 p=strrchr(ffdir,'/');
599 p = (ffdir[0]=='.' || p==NULL) ? ffdir : p+1;
600 fprintf(out,"#include \"%s/%s.itp\"\n",p,water);
603 fprintf(out,"#ifdef POSRES_WATER\n");
604 fprintf(out,"; Position restraint for each water oxygen\n");
605 fprintf(out,"[ position_restraints ]\n");
606 fprintf(out,";%3s %5s %9s %10s %10s\n","i","funct","fcx","fcy","fcz");
607 fprintf(out,"%4d %4d %10g %10g %10g\n",1,1,1000.0,1000.0,1000.0);
608 fprintf(out,"#endif\n");
611 sprintf(buf,"%s/ions.itp",p);
613 if (fflib_fexist(buf))
615 fprintf(out,"; Include topology for ions\n");
616 fprintf(out,"#include \"%s\"\n",buf);
621 static void print_top_system(FILE *out, const char *title)
623 fprintf(out,"[ %s ]\n",dir2str(d_system));
624 fprintf(out,"; Name\n");
625 fprintf(out,"%s\n\n",title[0]?title:"Protein");
628 void print_top_mols(FILE *out,
629 const char *title, const char *ffdir, const char *water,
630 int nincl, char **incls, int nmol, t_mols *mols)
636 fprintf(out,"; Include chain topologies\n");
637 for (i=0; (i<nincl); i++) {
638 incl = strrchr(incls[i],DIR_SEPARATOR);
642 /* Remove the path from the include name */
645 fprintf(out,"#include \"%s\"\n",incl);
652 print_top_water(out,ffdir,water);
654 print_top_system(out, title);
657 fprintf(out,"[ %s ]\n",dir2str(d_molecules));
658 fprintf(out,"; %-15s %5s\n","Compound","#mols");
659 for (i=0; (i<nmol); i++)
660 fprintf(out,"%-15s %5d\n",mols[i].name,mols[i].nr);
664 void write_top(FILE *out, char *pr,char *molname,
665 t_atoms *at,gmx_bool bRTPresname,
666 int bts[],t_params plist[],t_excls excls[],
667 gpp_atomtype_t atype,int *cgnr, int nrexcl)
668 /* NOTE: nrexcl is not the size of *excl! */
670 if (at && atype && cgnr) {
671 fprintf(out,"[ %s ]\n",dir2str(d_moleculetype));
672 fprintf(out,"; %-15s %5s\n","Name","nrexcl");
673 fprintf(out,"%-15s %5d\n\n",molname?molname:"Protein",nrexcl);
675 print_atoms(out, atype, at, cgnr, bRTPresname);
676 print_bondeds(out,at->nr,d_bonds, F_BONDS, bts[ebtsBONDS], plist);
677 print_bondeds(out,at->nr,d_constraints,F_CONSTR, 0, plist);
678 print_bondeds(out,at->nr,d_constraints,F_CONSTRNC, 0, plist);
679 print_bondeds(out,at->nr,d_pairs, F_LJ14, 0, plist);
680 print_excl(out,at->nr,excls);
681 print_bondeds(out,at->nr,d_angles, F_ANGLES, bts[ebtsANGLES],plist);
682 print_bondeds(out,at->nr,d_dihedrals, F_PDIHS, bts[ebtsPDIHS], plist);
683 print_bondeds(out,at->nr,d_dihedrals, F_IDIHS, bts[ebtsIDIHS], plist);
684 print_bondeds(out,at->nr,d_cmap, F_CMAP, bts[ebtsCMAP], plist);
685 print_bondeds(out,at->nr,d_polarization,F_POLARIZATION, 0, plist);
686 print_bondeds(out,at->nr,d_thole_polarization,F_THOLE_POL,0, plist);
687 print_bondeds(out,at->nr,d_vsites2, F_VSITE2, 0, plist);
688 print_bondeds(out,at->nr,d_vsites3, F_VSITE3, 0, plist);
689 print_bondeds(out,at->nr,d_vsites3, F_VSITE3FD, 0, plist);
690 print_bondeds(out,at->nr,d_vsites3, F_VSITE3FAD,0, plist);
691 print_bondeds(out,at->nr,d_vsites3, F_VSITE3OUT,0, plist);
692 print_bondeds(out,at->nr,d_vsites4, F_VSITE4FD, 0, plist);
693 print_bondeds(out,at->nr,d_vsites4, F_VSITE4FDN, 0, plist);
696 print_top_posre(out,pr);
700 static atom_id search_res_atom(const char *type,int resind,
702 const char *bondtype,gmx_bool bAllowMissing)
706 for(i=0; (i<atoms->nr); i++)
708 if (atoms->atom[i].resind == resind)
710 return search_atom(type,i,atoms,bondtype,bAllowMissing);
717 static void do_ssbonds(t_params *ps,t_atoms *atoms,
718 int nssbonds,t_ssbond *ssbonds,gmx_bool bAllowMissing)
723 for(i=0; (i<nssbonds); i++) {
724 ri = ssbonds[i].res1;
725 rj = ssbonds[i].res2;
726 ai = search_res_atom(ssbonds[i].a1,ri,atoms,
727 "special bond",bAllowMissing);
728 aj = search_res_atom(ssbonds[i].a2,rj,atoms,
729 "special bond",bAllowMissing);
730 if ((ai == NO_ATID) || (aj == NO_ATID))
731 gmx_fatal(FARGS,"Trying to make impossible special bond (%s-%s)!",
732 ssbonds[i].a1,ssbonds[i].a2);
733 add_param(ps,ai,aj,NULL,NULL);
737 static void at2bonds(t_params *psb, t_hackblock *hb,
740 real long_bond_dist, real short_bond_dist,
741 gmx_bool bAllowMissing)
745 real dist2, long_bond_dist2, short_bond_dist2;
748 long_bond_dist2 = sqr(long_bond_dist);
749 short_bond_dist2 = sqr(short_bond_dist);
756 fprintf(stderr,"Making bonds...\n");
758 for(resind=0; (resind < atoms->nres) && (i<atoms->nr); resind++) {
759 /* add bonds from list of bonded interactions */
760 for(j=0; j < hb[resind].rb[ebtsBONDS].nb; j++) {
761 /* Unfortunately we can not issue errors or warnings
762 * for missing atoms in bonds, as the hydrogens and terminal atoms
763 * have not been added yet.
765 ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,atoms,
767 aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,atoms,
769 if (ai != NO_ATID && aj != NO_ATID) {
770 dist2 = distance2(x[ai],x[aj]);
771 if (dist2 > long_bond_dist2 )
773 fprintf(stderr,"Warning: Long Bond (%d-%d = %g nm)\n",
774 ai+1,aj+1,sqrt(dist2));
776 else if (dist2 < short_bond_dist2 )
778 fprintf(stderr,"Warning: Short Bond (%d-%d = %g nm)\n",
779 ai+1,aj+1,sqrt(dist2));
781 add_param(psb,ai,aj,NULL,hb[resind].rb[ebtsBONDS].b[j].s);
784 /* add bonds from list of hacks (each added atom gets a bond) */
785 while( (i<atoms->nr) && (atoms->atom[i].resind == resind) ) {
786 for(j=0; j < hb[resind].nhack; j++)
787 if ( ( hb[resind].hack[j].tp > 0 ||
788 hb[resind].hack[j].oname==NULL ) &&
789 strcmp(hb[resind].hack[j].AI,*(atoms->atomname[i])) == 0 ) {
790 switch(hb[resind].hack[j].tp) {
791 case 9: /* COOH terminus */
792 add_param(psb,i,i+1,NULL,NULL); /* C-O */
793 add_param(psb,i,i+2,NULL,NULL); /* C-OA */
794 add_param(psb,i+2,i+3,NULL,NULL); /* OA-H */
797 for(k=0; (k<hb[resind].hack[j].nr); k++)
798 add_param(psb,i,i+k+1,NULL,NULL);
803 /* we're now at the start of the next residue */
807 static int pcompar(const void *a, const void *b)
818 return strlen(pb->s) - strlen(pa->s);
823 static void clean_bonds(t_params *ps)
829 /* swap atomnumbers in bond if first larger than second: */
830 for(i=0; (i<ps->nr); i++)
831 if ( ps->param[i].AJ < ps->param[i].AI ) {
833 ps->param[i].AI = ps->param[i].AJ;
838 qsort(ps->param,ps->nr,(size_t)sizeof(ps->param[0]),pcompar);
840 /* remove doubles, keep the first one always. */
842 for(i=1; (i<ps->nr); i++) {
843 if ((ps->param[i].AI != ps->param[j-1].AI) ||
844 (ps->param[i].AJ != ps->param[j-1].AJ) ) {
846 cp_param(&(ps->param[j]),&(ps->param[i]));
851 fprintf(stderr,"Number of bonds was %d, now %d\n",ps->nr,j);
855 fprintf(stderr,"No bonds\n");
858 void print_sums(t_atoms *atoms, gmx_bool bSystem)
871 for(i=0; (i<atoms->nr); i++) {
873 qtot+=atoms->atom[i].q;
876 fprintf(stderr,"Total mass%s %.3f a.m.u.\n",where,m);
877 fprintf(stderr,"Total charge%s %.3f e\n",where,qtot);
880 static void check_restp_type(const char *name,int t1,int t2)
884 gmx_fatal(FARGS,"Residues in one molecule have a different '%s' type: %d and %d",name,t1,t2);
888 static void check_restp_types(t_restp *r0,t_restp *r1)
892 check_restp_type("all dihedrals",r0->bAlldih,r1->bAlldih);
893 check_restp_type("nrexcl",r0->nrexcl,r1->nrexcl);
894 check_restp_type("HH14",r0->HH14,r1->HH14);
895 check_restp_type("remove dihedrals",r0->bRemoveDih,r1->bRemoveDih);
897 for(i=0; i<ebtsNR; i++)
899 check_restp_type(btsNames[i],r0->rb[i].type,r1->rb[i].type);
903 void add_atom_to_restp(t_restp *restp,int resnr,int at_start,const t_hack *hack)
907 const char *Hnum="123456";
911 fprintf(debug,"adding atom(s) %s to atom %s in res %d%s in rtp\n",
913 *restp->atomname[at_start], resnr, restp->resname);
915 strcpy(buf, hack->nname);
916 buf[strlen(buf)+1]='\0';
919 buf[strlen(buf)]='-';
922 restp->natom += hack->nr;
923 srenew(restp->atom, restp->natom);
924 srenew(restp->atomname, restp->natom);
925 srenew(restp->cgnr, restp->natom);
927 for(k=restp->natom-1; k > at_start+hack->nr; k--)
930 restp->atom [k - hack->nr];
932 restp->atomname[k - hack->nr];
934 restp->cgnr [k - hack->nr];
937 for(k=0; k < hack->nr; k++)
939 /* set counter in atomname */
942 buf[strlen(buf)-1] = Hnum[k];
944 snew( restp->atomname[at_start+1+k], 1);
945 restp->atom [at_start+1+k] = *hack->atom;
946 *restp->atomname[at_start+1+k] = strdup(buf);
947 if ( hack->cgnr != NOTSET )
949 restp->cgnr [at_start+1+k] = hack->cgnr;
953 restp->cgnr [at_start+1+k] = restp->cgnr[at_start];
958 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
959 int nrtp, t_restp rtp[],
960 int nres, t_resinfo *resinfo,
962 t_hackblock **ntdb, t_hackblock **ctdb,
969 const char *Hnum="123456";
975 /* first the termini */
976 for(i=0; i<nterpairs; i++) {
977 if (rn[i] >= 0 && ntdb[i] != NULL) {
978 copy_t_hackblock(ntdb[i], &(*hb)[rn[i]]);
980 if (rc[i] >= 0 && ctdb[i] != NULL) {
981 merge_t_hackblock(ctdb[i], &(*hb)[rc[i]]);
985 /* then the whole rtp */
986 for(i=0; i < nres; i++) {
987 /* Here we allow a mismatch of one character when looking for the rtp entry.
988 * For such a mismatch there should be only one mismatching name.
989 * This is mainly useful for small molecules such as ions.
990 * Note that this will usually not work for protein, DNA and RNA,
991 * since there the residue names should be listed in residuetypes.dat
992 * and an error will have been generated earlier in the process.
994 key = *resinfo[i].rtp;
995 snew(resinfo[i].rtp,1);
996 *resinfo[i].rtp = search_rtp(key,nrtp,rtp);
997 res = get_restp(*resinfo[i].rtp,nrtp,rtp);
998 copy_t_restp(res, &(*restp)[i]);
1000 /* Check that we do not have different bonded types in one molecule */
1001 check_restp_types(&(*restp)[0],&(*restp)[i]);
1004 for(j=0; j<nterpairs && tern==-1; j++) {
1010 for(j=0; j<nterpairs && terc == -1; j++) {
1015 bRM = merge_t_bondeds(res->rb, (*hb)[i].rb,tern>=0,terc>=0);
1017 if (bRM && ((tern >= 0 && ntdb[tern] == NULL) ||
1018 (terc >= 0 && ctdb[terc] == NULL))) {
1019 gmx_fatal(FARGS,"There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.");
1021 if (bRM && ((tern >= 0 && ntdb[tern]->nhack == 0) ||
1022 (terc >= 0 && ctdb[terc]->nhack == 0))) {
1023 gmx_fatal(FARGS,"There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.");
1027 /* now perform t_hack's on t_restp's,
1028 i.e. add's and deletes from termini database will be
1029 added to/removed from residue topology
1030 we'll do this on one big dirty loop, so it won't make easy reading! */
1031 for(i=0; i < nres; i++)
1033 for(j=0; j < (*hb)[i].nhack; j++)
1035 if ( (*hb)[i].hack[j].nr )
1037 /* find atom in restp */
1038 for(l=0; l < (*restp)[i].natom; l++)
1039 if ( ( (*hb)[i].hack[j].oname==NULL &&
1040 strcmp((*hb)[i].hack[j].AI, *(*restp)[i].atomname[l])==0 ) ||
1041 ( (*hb)[i].hack[j].oname!=NULL &&
1042 strcmp((*hb)[i].hack[j].oname,*(*restp)[i].atomname[l])==0 ) )
1044 if (l == (*restp)[i].natom)
1046 /* If we are doing an atom rename only, we don't need
1047 * to generate a fatal error if the old name is not found
1050 /* Deleting can happen also only on the input atoms,
1051 * not necessarily always on the rtp entry.
1053 if (!((*hb)[i].hack[j].oname != NULL &&
1054 (*hb)[i].hack[j].nname != NULL) &&
1055 !((*hb)[i].hack[j].oname != NULL &&
1056 (*hb)[i].hack[j].nname == NULL))
1059 "atom %s not found in buiding block %d%s "
1060 "while combining tdb and rtp",
1061 (*hb)[i].hack[j].oname!=NULL ?
1062 (*hb)[i].hack[j].oname : (*hb)[i].hack[j].AI,
1063 i+1,*resinfo[i].rtp);
1068 if ( (*hb)[i].hack[j].oname==NULL ) {
1070 add_atom_to_restp(&(*restp)[i],resinfo[i].nr,l,
1076 if ( (*hb)[i].hack[j].nname==NULL ) {
1077 /* we're deleting */
1079 fprintf(debug, "deleting atom %s from res %d%s in rtp\n",
1080 *(*restp)[i].atomname[l],
1081 i+1,(*restp)[i].resname);
1082 /* shift the rest */
1083 (*restp)[i].natom--;
1084 for(k=l; k < (*restp)[i].natom; k++) {
1085 (*restp)[i].atom [k] = (*restp)[i].atom [k+1];
1086 (*restp)[i].atomname[k] = (*restp)[i].atomname[k+1];
1087 (*restp)[i].cgnr [k] = (*restp)[i].cgnr [k+1];
1089 /* give back space */
1090 srenew((*restp)[i].atom, (*restp)[i].natom);
1091 srenew((*restp)[i].atomname, (*restp)[i].natom);
1092 srenew((*restp)[i].cgnr, (*restp)[i].natom);
1093 } else { /* nname != NULL */
1094 /* we're replacing */
1096 fprintf(debug, "replacing atom %s by %s in res %d%s in rtp\n",
1097 *(*restp)[i].atomname[l], (*hb)[i].hack[j].nname,
1098 i+1,(*restp)[i].resname);
1099 snew( (*restp)[i].atomname[l], 1);
1100 (*restp)[i].atom[l] = *(*hb)[i].hack[j].atom;
1101 *(*restp)[i].atomname[l] = strdup((*hb)[i].hack[j].nname);
1102 if ( (*hb)[i].hack[j].cgnr != NOTSET )
1103 (*restp)[i].cgnr [l] = (*hb)[i].hack[j].cgnr;
1112 static gmx_bool atomname_cmp_nr(const char *anm,t_hack *hack,int *nr)
1119 return (gmx_strcasecmp(anm,hack->nname) == 0);
1123 if (isdigit(anm[strlen(anm)-1]))
1125 *nr = anm[strlen(anm)-1] - '0';
1131 if (*nr <= 0 || *nr > hack->nr)
1137 return (strlen(anm) == strlen(hack->nname) + 1 &&
1138 gmx_strncasecmp(anm,hack->nname,strlen(hack->nname)) == 0);
1143 static gmx_bool match_atomnames_with_rtp_atom(t_atoms *pdba,rvec *x,int atind,
1144 t_restp *rptr,t_hackblock *hbr,
1151 char *start_at,buf[STRLEN];
1153 gmx_bool bReplaceReplace,bFoundInAdd;
1156 oldnm = *pdba->atomname[atind];
1157 resnr = pdba->resinfo[pdba->atom[atind].resind].nr;
1160 for(j=0; j<hbr->nhack; j++)
1162 if (hbr->hack[j].oname != NULL && hbr->hack[j].nname != NULL &&
1163 gmx_strcasecmp(oldnm,hbr->hack[j].oname) == 0)
1165 /* This is a replace entry. */
1166 /* Check if we are not replacing a replaced atom. */
1167 bReplaceReplace = FALSE;
1168 for(k=0; k<hbr->nhack; k++) {
1170 hbr->hack[k].oname != NULL && hbr->hack[k].nname != NULL &&
1171 gmx_strcasecmp(hbr->hack[k].nname,hbr->hack[j].oname) == 0)
1173 /* The replace in hack[j] replaces an atom that
1174 * was already replaced in hack[k], we do not want
1175 * second or higher level replaces at this stage.
1177 bReplaceReplace = TRUE;
1180 if (bReplaceReplace)
1182 /* Skip this replace. */
1186 /* This atom still has the old name, rename it */
1187 newnm = hbr->hack[j].nname;
1188 for(k=0; k<rptr->natom; k++)
1190 if (gmx_strcasecmp(newnm,*rptr->atomname[k]) == 0)
1195 if (k == rptr->natom)
1197 /* The new name is not present in the rtp.
1198 * We need to apply the replace also to the rtp entry.
1201 /* We need to find the add hack that can add this atom
1202 * to find out after which atom it should be added.
1204 bFoundInAdd = FALSE;
1205 for(k=0; k<hbr->nhack; k++)
1207 if (hbr->hack[k].oname == NULL &&
1208 hbr->hack[k].nname != NULL &&
1209 atomname_cmp_nr(newnm,&hbr->hack[k],&anmnr))
1213 start_at = hbr->hack[k].a[0];
1217 sprintf(buf,"%s%d",hbr->hack[k].nname,anmnr-1);
1220 for(start_nr=0; start_nr<rptr->natom; start_nr++)
1222 if (gmx_strcasecmp(start_at,(*rptr->atomname[start_nr])) == 0)
1227 if (start_nr == rptr->natom)
1229 gmx_fatal(FARGS,"Could not find atom '%s' in residue building block '%s' to add atom '%s' to",
1230 start_at,rptr->resname,newnm);
1232 /* We can add the atom after atom start_nr */
1233 add_atom_to_restp(rptr,resnr,start_nr,
1242 gmx_fatal(FARGS,"Could not find an 'add' entry for atom named '%s' corresponding to the 'replace' entry from atom name '%s' to '%s' for tdb or hdb database of residue type '%s'",
1244 hbr->hack[j].oname,hbr->hack[j].nname,
1251 printf("Renaming atom '%s' in residue '%s' %d to '%s'\n",
1252 oldnm,rptr->resname,resnr,newnm);
1254 /* Rename the atom in pdba */
1255 snew(pdba->atomname[atind],1);
1256 *pdba->atomname[atind] = strdup(newnm);
1258 else if (hbr->hack[j].oname != NULL && hbr->hack[j].nname == NULL &&
1259 gmx_strcasecmp(oldnm,hbr->hack[j].oname) == 0)
1261 /* This is a delete entry, check if this atom is present
1262 * in the rtp entry of this residue.
1264 for(k=0; k<rptr->natom; k++)
1266 if (gmx_strcasecmp(oldnm,*rptr->atomname[k]) == 0)
1271 if (k == rptr->natom)
1273 /* This atom is not present in the rtp entry,
1274 * delete is now from the input pdba.
1278 printf("Deleting atom '%s' in residue '%s' %d\n",
1279 oldnm,rptr->resname,resnr);
1281 /* We should free the atom name,
1282 * but it might be used multiple times in the symtab.
1283 * sfree(pdba->atomname[atind]);
1285 for(k=atind+1; k<pdba->nr; k++)
1287 pdba->atom[k-1] = pdba->atom[k];
1288 pdba->atomname[k-1] = pdba->atomname[k];
1289 copy_rvec(x[k],x[k-1]);
1300 void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
1301 t_atoms *pdba,rvec *x,
1310 char *start_at,buf[STRLEN];
1312 gmx_bool bFoundInAdd;
1314 for(i=0; i<pdba->nr; i++)
1316 oldnm = *pdba->atomname[i];
1317 resnr = pdba->resinfo[pdba->atom[i].resind].nr;
1318 rptr = &restp[pdba->atom[i].resind];
1319 for(j=0; (j<rptr->natom); j++)
1321 if (gmx_strcasecmp(oldnm,*(rptr->atomname[j])) == 0)
1326 if (j == rptr->natom)
1328 /* Not found yet, check if we have to rename this atom */
1329 if (match_atomnames_with_rtp_atom(pdba,x,i,
1330 rptr,&(hb[pdba->atom[i].resind]),
1333 /* We deleted this atom, decrease the atom counter by 1. */
1340 #define NUM_CMAP_ATOMS 5
1341 static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuetype_t rt)
1345 t_resinfo *resinfo = atoms->resinfo;
1346 int nres = atoms->nres;
1348 atom_id cmap_atomid[NUM_CMAP_ATOMS];
1349 int cmap_chainnum=-1, this_residue_index;
1356 fprintf(stderr,"Making cmap torsions...");
1358 /* End loop at nres-1, since the very last residue does not have a +N atom, and
1359 * therefore we get a valgrind invalid 4 byte read error with atom am */
1360 for(residx=0; residx<nres-1; residx++)
1362 /* Add CMAP terms from the list of CMAP interactions */
1363 for(j=0;j<restp[residx].rb[ebtsCMAP].nb; j++)
1366 /* Loop over atoms in a candidate CMAP interaction and
1367 * check that they exist, are from the same chain and are
1368 * from residues labelled as protein. */
1369 for(k = 0; k < NUM_CMAP_ATOMS && bAddCMAP; k++)
1371 cmap_atomid[k] = search_atom(restp[residx].rb[ebtsCMAP].b[j].a[k],
1373 bAddCMAP = bAddCMAP && (cmap_atomid[k] != NO_ATID);
1376 /* This break is necessary, because cmap_atomid[k]
1377 * == NO_ATID cannot be safely used as an index
1378 * into the atom array. */
1381 this_residue_index = atoms->atom[cmap_atomid[k]].resind;
1384 cmap_chainnum = resinfo[this_residue_index].chainnum;
1388 /* Does the residue for this atom have the same
1389 * chain number as the residues for previous
1391 bAddCMAP = bAddCMAP &&
1392 cmap_chainnum == resinfo[this_residue_index].chainnum;
1394 bAddCMAP = bAddCMAP && gmx_residuetype_is_protein(rt,*(resinfo[this_residue_index].name));
1399 add_cmap_param(psb,cmap_atomid[0],cmap_atomid[1],cmap_atomid[2],cmap_atomid[3],cmap_atomid[4],restp[residx].rb[ebtsCMAP].b[j].s);
1405 while(atoms->atom[i].resind<residx+1)
1412 /* Start the next residue */
1416 scrub_charge_groups(int *cgnr, int natoms)
1420 for(i=0;i<natoms;i++)
1427 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
1428 t_atoms *atoms, rvec **x, gpp_atomtype_t atype, t_symtab *tab,
1429 int nrtp, t_restp rtp[],
1430 t_restp *restp, t_hackblock *hb,
1431 int nterpairs,t_hackblock **ntdb, t_hackblock **ctdb,
1432 gmx_bool bAllowMissing,
1433 gmx_bool bVsites, gmx_bool bVsiteAromatics,
1434 const char *ff, const char *ffdir,
1436 int nssbonds, t_ssbond *ssbonds,
1437 real long_bond_dist, real short_bond_dist,
1438 gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
1439 gmx_bool bRenumRes,gmx_bool bRTPresname)
1445 t_params plist[F_NRE];
1452 gmx_residuetype_t rt;
1455 gmx_residuetype_init(&rt);
1458 print_resall(debug, atoms->nres, restp, atype);
1459 dump_hb(debug, atoms->nres, hb);
1463 at2bonds(&(plist[F_BONDS]), hb,
1465 long_bond_dist, short_bond_dist, bAllowMissing);
1467 /* specbonds: disulphide bonds & heme-his */
1468 do_ssbonds(&(plist[F_BONDS]),
1469 atoms, nssbonds, ssbonds,
1472 nmissat = name2type(atoms, &cgnr, atype, restp, rt);
1475 fprintf(stderr,"There were %d missing atoms in molecule %s\n",
1478 gmx_fatal(FARGS,"There were %d missing atoms in molecule %s, if you want to use this incomplete topology anyhow, use the option -missing",
1482 /* Cleanup bonds (sort and rm doubles) */
1483 clean_bonds(&(plist[F_BONDS]));
1485 snew(vsite_type,atoms->nr);
1486 for(i=0; i<atoms->nr; i++)
1487 vsite_type[i]=NOTSET;
1489 /* determine which atoms will be vsites and add dummy masses
1490 also renumber atom numbers in plist[0..F_NRE]! */
1491 do_vsites(nrtp, rtp, atype, atoms, tab, x, plist,
1492 &vsite_type, &cgnr, mHmult, bVsiteAromatics, ffdir);
1495 /* Make Angles and Dihedrals */
1496 fprintf(stderr,"Generating angles, dihedrals and pairs...\n");
1497 snew(excls,atoms->nr);
1498 init_nnb(&nnb,atoms->nr,4);
1499 gen_nnb(&nnb,plist);
1500 print_nnb(&nnb,"NNB");
1501 gen_pad(&nnb,atoms,restp[0].nrexcl,restp[0].HH14,
1502 plist,excls,hb,restp[0].bAlldih,restp[0].bRemoveDih,
1509 gen_cmap(&(plist[F_CMAP]), restp, atoms, rt);
1510 if (plist[F_CMAP].nr > 0)
1512 fprintf(stderr, "There are %4d cmap torsion pairs\n",
1517 /* set mass of all remaining hydrogen atoms */
1519 do_h_mass(&(plist[F_BONDS]),vsite_type,atoms,mHmult,bDeuterate);
1522 /* Cleanup bonds (sort and rm doubles) */
1523 /* clean_bonds(&(plist[F_BONDS]));*/
1526 "There are %4d dihedrals, %4d impropers, %4d angles\n"
1527 " %4d pairs, %4d bonds and %4d virtual sites\n",
1528 plist[F_PDIHS].nr, plist[F_IDIHS].nr, plist[F_ANGLES].nr,
1529 plist[F_LJ14].nr, plist[F_BONDS].nr,
1530 plist[F_VSITE2].nr +
1531 plist[F_VSITE3].nr +
1532 plist[F_VSITE3FD].nr +
1533 plist[F_VSITE3FAD].nr +
1534 plist[F_VSITE3OUT].nr +
1535 plist[F_VSITE4FD].nr +
1536 plist[F_VSITE4FDN].nr );
1538 print_sums(atoms, FALSE);
1540 if (FALSE == bChargeGroups)
1542 scrub_charge_groups(cgnr, atoms->nr);
1547 for(i=0; i<atoms->nres; i++)
1549 atoms->resinfo[i].nr = i + 1;
1550 atoms->resinfo[i].ic = ' ';
1555 fprintf(stderr,"Writing topology\n");
1556 /* We can copy the bonded types from the first restp,
1557 * since the types have to be identical for all residues in one molecule.
1559 for(i=0; i<ebtsNR; i++) {
1560 bts[i] = restp[0].rb[i].type;
1562 write_top(top_file, posre_fn, molname,
1564 bts, plist, excls, atype, cgnr, restp[0].nrexcl);
1568 free_t_hackblock(atoms->nres, &hb);
1569 free_t_restp(atoms->nres, &restp);
1570 gmx_residuetype_destroy(rt);
1572 /* we should clean up hb and restp here, but that is a *L*O*T* of work! */
1574 for (i=0; i<F_NRE; i++)
1575 sfree(plist[i].param);
1576 for (i=0; i<atoms->nr; i++)