src/kernel/pdb2top.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  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.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
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  19  * of the License, or (at your option) any later version.
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  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <stdio.h>
  41 #include <math.h>
  42 #include <ctype.h>
  43
  44 #if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
  45 #include <direct.h>
  46 #include <io.h>
  47 #endif
  48
  49
  50 #include "vec.h"
  51 #include "copyrite.h"
  52 #include "smalloc.h"
  53 #include "macros.h"
  54 #include "symtab.h"
  55 #include "futil.h"
  56 #include "statutil.h"
  57 #include "gmx_fatal.h"
  58 #include "pdb2top.h"
  59 #include "gpp_nextnb.h"
  60 #include "topdirs.h"
  61 #include "toputil.h"
  62 #include "h_db.h"
  63 #include "pgutil.h"
  64 #include "resall.h"
  65 #include "topio.h"
  66 #include "string2.h"
  67 #include "physics.h"
  68 #include "pdbio.h"
  69 #include "gen_ad.h"
  70 #include "filenm.h"
  71 #include "index.h"
  72 #include "gen_vsite.h"
  73 #include "add_par.h"
  74 #include "toputil.h"
  75 #include "fflibutil.h"
  76 #include "strdb.h"
  77
  78 /* this must correspond to enum in pdb2top.h */
  79 const char *hh[ehisNR]   = { "HISD", "HISE", "HISH", "HIS1" };
  80
  81 static int missing_atoms(t_restp *rp, int resind,t_atoms *at, int i0, int i)
  82 {
  83     int  j,k,nmiss;
  84     char *name;
  85     gmx_bool bFound, bRet;
  86
  87     nmiss = 0;
  88     for (j=0; j<rp->natom; j++)
  89     {
  90         name=*(rp->atomname[j]);
  91         bFound=FALSE;
  92         for (k=i0; k<i; k++)
  93         {
  94             bFound = (bFound || !gmx_strcasecmp(*(at->atomname[k]),name));
  95         }
  96         if (!bFound)
  97         {
  98             nmiss++;
  99             fprintf(stderr,"\nWARNING: "
 100                     "atom %s is missing in residue %s %d in the pdb file\n",
 101                     name,*(at->resinfo[resind].name),at->resinfo[resind].nr);
 102             if (name[0]=='H' || name[0]=='h')
 103             {
 104                 fprintf(stderr,"         You might need to add atom %s to the hydrogen database of building block %s\n"
 105                         "         in the file %s.hdb (see the manual)\n",
 106                         name,*(at->resinfo[resind].rtp),rp->filebase);
 107             }
 108             fprintf(stderr,"\n");
 109         }
 110     }
 111
 112     return nmiss;
 113 }
 114
 115 gmx_bool is_int(double x)
 116 {
 117   const double tol = 1e-4;
 118   int   ix;
 119
 120   if (x < 0)
 121     x=-x;
 122   ix=gmx_nint(x);
 123
 124   return (fabs(x-ix) < tol);
 125 }
 126
 127 static void swap_strings(char **s,int i,int j)
 128 {
 129     char *tmp;
 130
 131     tmp  = s[i];
 132     s[i] = s[j];
 133     s[j] = tmp;
 134 }
 135
 136 void
 137 choose_ff(const char *ffsel,
 138           char *forcefield, int ff_maxlen,
 139           char *ffdir, int ffdir_maxlen)
 140 {
 141     int  nff;
 142     char **ffdirs,**ffs,**ffs_dir,*ptr;
 143     int  i,j,sel,cwdsel,nfound;
 144     char buf[STRLEN],**desc;
 145     FILE *fp;
 146     char *pret;
 147
 148     nff = fflib_search_file_in_dirend(fflib_forcefield_itp(),
 149                                       fflib_forcefield_dir_ext(),
 150                                       &ffdirs);
 151
 152     if (nff == 0)
 153     {
 154         gmx_fatal(FARGS,"No force fields found (files with name '%s' in subdirectories ending on '%s')",
 155                   fflib_forcefield_itp(),fflib_forcefield_dir_ext());
 156     }
 157
 158     /* Replace with unix path separators */
 159     if(DIR_SEPARATOR!='/')
 160     {
 161         for(i=0;i<nff;i++)
 162         {
 163             while( (ptr=strchr(ffdirs[i],DIR_SEPARATOR))!=NULL )
 164             {
 165                 *ptr='/';
 166             }
 167         }
 168     }
 169
 170     /* Store the force field names in ffs */
 171     snew(ffs,nff);
 172     snew(ffs_dir,nff);
 173     for(i=0; i<nff; i++)
 174     {
 175         /* Remove the path from the ffdir name - use our unix standard here! */
 176         ptr = strrchr(ffdirs[i],'/');
 177         if (ptr == NULL)
 178         {
 179             ffs[i] = strdup(ffdirs[i]);
 180             ffs_dir[i] = low_gmxlibfn(ffdirs[i],FALSE,FALSE);
 181             if (ffs_dir[i] == NULL)
 182             {
 183                 gmx_fatal(FARGS,"Can no longer find file '%s'",ffdirs[i]);
 184             }
 185         }
 186         else
 187         {
 188             ffs[i] = strdup(ptr+1);
 189             ffs_dir[i] = strdup(ffdirs[i]);
 190         }
 191         ffs_dir[i][strlen(ffs_dir[i])-strlen(ffs[i])-1] = '\0';
 192         /* Remove the extension from the ffdir name */
 193         ffs[i][strlen(ffs[i])-strlen(fflib_forcefield_dir_ext())] = '\0';
 194     }
 195
 196     if (ffsel != NULL)
 197     {
 198         sel     = -1;
 199         cwdsel  = -1;
 200         nfound  = 0;
 201         for(i=0; i<nff; i++)
 202         {
 203             if ( strcmp(ffs[i],ffsel)==0 )
 204             {
 205                 /* Matching ff name */
 206                 sel = i;
 207                 nfound++;
 208
 209                 if( strncmp(ffs_dir[i],".",1)==0 )
 210                 {
 211                     cwdsel = i;
 212                 }
 213             }
 214         }
 215
 216         if(cwdsel != -1)
 217         {
 218             sel = cwdsel;
 219         }
 220
 221         if(nfound>1)
 222         {
 223             if(cwdsel!=-1)
 224             {
 225                 fprintf(stderr,
 226                         "Force field '%s' occurs in %d places. pdb2gmx is using the one in the\n"
 227                         "current directory. Use interactive selection (not the -ff option) if\n"
 228                         "you would prefer a different one.\n",ffsel,nfound);
 229             }
 230             else
 231             {
 232                 gmx_fatal(FARGS,
 233                           "Force field '%s' occurs in %d places, but not in the current directory.\n"
 234                           "Run without the -ff switch and select the force field interactively.",ffsel,nfound);
 235             }
 236         }
 237         else if (nfound==0)
 238         {
 239             gmx_fatal(FARGS,"Could not find force field '%s' in current directory, install tree or GMXDATA path.",ffsel);
 240         }
 241     }
 242     else if (nff > 1)
 243     {
 244         snew(desc,nff);
 245         for(i=0; (i<nff); i++)
 246         {
 247             sprintf(buf,"%s%c%s%s%c%s",
 248                     ffs_dir[i],DIR_SEPARATOR,
 249                     ffs[i],fflib_forcefield_dir_ext(),DIR_SEPARATOR,
 250                     fflib_forcefield_doc());
 251             if (gmx_fexist(buf))
 252             {
 253                 /* We don't use fflib_open, because we don't want printf's */
 254                 fp = ffopen(buf,"r");
 255                 snew(desc[i],STRLEN);
 256                 get_a_line(fp,desc[i],STRLEN);
 257                 ffclose(fp);
 258             }
 259             else
 260             {
 261                 desc[i] = strdup(ffs[i]);
 262             }
 263         }
 264         /* Order force fields from the same dir alphabetically
 265          * and put deprecated force fields at the end.
 266          */
 267         for(i=0; (i<nff); i++)
 268         {
 269             for(j=i+1; (j<nff); j++)
 270             {
 271                 if (strcmp(ffs_dir[i],ffs_dir[j]) == 0 &&
 272                     ((desc[i][0] == '[' && desc[j][0] != '[') ||
 273                      ((desc[i][0] == '[' || desc[j][0] != '[') &&
 274                       gmx_strcasecmp(desc[i],desc[j]) > 0)))
 275                 {
 276                     swap_strings(ffdirs,i,j);
 277                     swap_strings(ffs   ,i,j);
 278                     swap_strings(desc  ,i,j);
 279                 }
 280             }
 281         }
 282
 283         printf("\nSelect the Force Field:\n");
 284         for(i=0; (i<nff); i++)
 285         {
 286             if (i == 0 || strcmp(ffs_dir[i-1],ffs_dir[i]) != 0)
 287             {
 288                 if( strcmp(ffs_dir[i],".")==0 )
 289                 {
 290                     printf("From current directory:\n");
 291                 }
 292                 else
 293                 {
 294                     printf("From '%s':\n",ffs_dir[i]);
 295                 }
 296             }
 297             printf("%2d: %s\n",i+1,desc[i]);
 298             sfree(desc[i]);
 299         }
 300         sfree(desc);
 301
 302         do
 303         {
 304             pret = fgets(buf,STRLEN,stdin);
 305
 306             if (pret != NULL)
 307             {
 308                 sscanf(buf,"%d",&sel);
 309                 sel--;
 310             }
 311         }
 312         while ( pret==NULL || (sel < 0) || (sel >= nff));
 313     }
 314     else
 315     {
 316         sel = 0;
 317     }
 318
 319     if (strlen(ffs[sel]) >= (size_t)ff_maxlen)
 320     {
 321         gmx_fatal(FARGS,"Length of force field name (%d) >= maxlen (%d)",
 322                   strlen(ffs[sel]),ff_maxlen);
 323     }
 324     strcpy(forcefield,ffs[sel]);
 325
 326     if (strlen(ffdirs[sel]) >= (size_t)ffdir_maxlen)
 327     {
 328         gmx_fatal(FARGS,"Length of force field dir (%d) >= maxlen (%d)",
 329                   strlen(ffdirs[sel]),ffdir_maxlen);
 330     }
 331     strcpy(ffdir,ffdirs[sel]);
 332
 333     for(i=0; (i<nff); i++)
 334     {
 335         sfree(ffdirs[i]);
 336         sfree(ffs[i]);
 337         sfree(ffs_dir[i]);
 338     }
 339     sfree(ffdirs);
 340     sfree(ffs);
 341     sfree(ffs_dir);
 342 }
 343
 344 void choose_watermodel(const char *wmsel,const char *ffdir,
 345                        char **watermodel)
 346 {
 347     const char *fn_watermodels="watermodels.dat";
 348     char fn_list[STRLEN];
 349     FILE *fp;
 350     char buf[STRLEN];
 351     int  nwm,sel,i;
 352     char **model;
 353     char *pret;
 354
 355     if (strcmp(wmsel,"none") == 0)
 356     {
 357         *watermodel = NULL;
 358
 359         return;
 360     }
 361     else if (strcmp(wmsel,"select") != 0)
 362     {
 363         *watermodel = strdup(wmsel);
 364
 365         return;
 366     }
 367
 368     sprintf(fn_list,"%s%c%s",ffdir,DIR_SEPARATOR,fn_watermodels);
 369
 370     if (!fflib_fexist(fn_list))
 371     {
 372         fprintf(stderr,"No file '%s' found, will not include a water model\n",
 373                 fn_watermodels);
 374         *watermodel = NULL;
 375
 376         return;
 377     }
 378
 379     fp = fflib_open(fn_list);
 380     printf("\nSelect the Water Model:\n");
 381     nwm = 0;
 382     model = NULL;
 383     while (get_a_line(fp,buf,STRLEN))
 384     {
 385         srenew(model,nwm+1);
 386         snew(model[nwm],STRLEN);
 387         sscanf(buf,"%s%n",model[nwm],&i);
 388         if (i > 0)
 389         {
 390             ltrim(buf+i);
 391             fprintf(stderr,"%2d: %s\n",nwm+1,buf+i);
 392             nwm++;
 393         }
 394         else
 395         {
 396             sfree(model[nwm]);
 397         }
 398     }
 399     fclose(fp);
 400     fprintf(stderr,"%2d: %s\n",nwm+1,"None");
 401
 402     do
 403     {
 404         pret = fgets(buf,STRLEN,stdin);
 405
 406         if (pret != NULL)
 407         {
 408             sscanf(buf,"%d",&sel);
 409             sel--;
 410         }
 411     }
 412     while (pret == NULL || sel < 0 || sel > nwm);
 413
 414     if (sel == nwm)
 415     {
 416         *watermodel = NULL;
 417     }
 418     else
 419     {
 420         *watermodel = strdup(model[sel]);
 421     }
 422
 423     for(i=0; i<nwm; i++)
 424     {
 425         sfree(model[i]);
 426     }
 427     sfree(model);
 428 }
 429
 430 static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
 431                      t_restp restp[])
 432 {
 433   int     i,j,prevresind,resind,i0,prevcg,cg,curcg;
 434   char    *name;
 435   gmx_bool    bProt, bNterm;
 436   double  qt;
 437   int     nmissat;
 438   gmx_residuetype_t rt;
 439
 440   nmissat = 0;
 441
 442   resind=-1;
 443   bProt=FALSE;
 444   bNterm=FALSE;
 445   i0=0;
 446   snew(*cgnr,at->nr);
 447   qt=0;
 448   prevcg=NOTSET;
 449   curcg=0;
 450   cg=-1;
 451   j=NOTSET;
 452   gmx_residuetype_init(&rt);
 453
 454   for(i=0; (i<at->nr); i++) {
 455     prevresind=resind;
 456     if (at->atom[i].resind != resind) {
 457       resind = at->atom[i].resind;
 458       bProt = gmx_residuetype_is_protein(rt,*(at->resinfo[resind].name));
 459       bNterm=bProt && (resind == 0);
 460       if (resind > 0) {
 461           nmissat += missing_atoms(&restp[prevresind],prevresind,at,i0,i);
 462       }
 463       i0=i;
 464     }
 465     if (at->atom[i].m == 0) {
 466       if (debug)
 467         fprintf(debug,"atom %d%s: curcg=%d, prevcg=%d, cg=%d\n",
 468                 i+1,*(at->atomname[i]),curcg,prevcg,
 469                 j==NOTSET ? NOTSET : restp[resind].cgnr[j]);
 470       qt=0;
 471       prevcg=cg;
 472       name=*(at->atomname[i]);
 473       j=search_jtype(&restp[resind],name,bNterm);
 474       at->atom[i].type = restp[resind].atom[j].type;
 475       at->atom[i].q    = restp[resind].atom[j].q;
 476       at->atom[i].m    = get_atomtype_massA(restp[resind].atom[j].type,
 477                                             atype);
 478       cg = restp[resind].cgnr[j];
 479       /* A charge group number -1 signals a separate charge group
 480        * for this atom.
 481        */
 482       if ( (cg == -1) || (cg != prevcg) || (resind != prevresind) ) {
 483           curcg++;
 484       }
 485     } else {
 486       if (debug)
 487         fprintf(debug,"atom %d%s: curcg=%d, qt=%g, is_int=%d\n",
 488                 i+1,*(at->atomname[i]),curcg,qt,is_int(qt));
 489       cg=-1;
 490       if (is_int(qt)) {
 491         qt=0;
 492         curcg++;
 493       }
 494       qt+=at->atom[i].q;
 495     }
 496     (*cgnr)[i]=curcg;
 497     at->atom[i].typeB = at->atom[i].type;
 498     at->atom[i].qB    = at->atom[i].q;
 499     at->atom[i].mB    = at->atom[i].m;
 500   }
 501   nmissat += missing_atoms(&restp[resind],resind,at,i0,i);
 502
 503   gmx_residuetype_destroy(rt);
 504
 505   return nmissat;
 506 }
 507
 508 static void print_top_heavy_H(FILE *out, real mHmult)
 509 {
 510   if (mHmult == 2.0)
 511     fprintf(out,"; Using deuterium instead of hydrogen\n\n");
 512   else if (mHmult == 4.0)
 513     fprintf(out,"#define HEAVY_H\n\n");
 514   else if (mHmult != 1.0)
 515     fprintf(stderr,"WARNING: unsupported proton mass multiplier (%g) "
 516             "in pdb2top\n",mHmult);
 517 }
 518
 519 void print_top_comment(FILE *out,
 520                        const char *filename,
 521                        const char *generator,
 522                        const char *ffdir,
 523                        gmx_bool bITP)
 524 {
 525   char tmp[256];
 526   char ffdir_parent[STRLEN];
 527   char *p;
 528
 529   nice_header(out,filename);
 530   fprintf(out,";\tThis is a %s topology file\n;\n",bITP ? "include" : "standalone");
 531   fprintf(out,";\tIt was generated using program:\n;\t%s\n;\n",
 532           (NULL == generator) ? "unknown" : generator);
 533   fprintf(out,";\tCommand line was:\n;\t%s\n;\n",command_line());
 534
 535   if(strchr(ffdir,'/')==NULL)
 536   {
 537       fprintf(out,";\tForce field was read from the standard Gromacs share directory.\n;\n\n");
 538   }
 539   else if(ffdir[0]=='.')
 540   {
 541       fprintf(out,";\tForce field was read from current directory or a relative path - path added.\n;\n\n");
 542   }
 543   else
 544   {
 545       strncpy(ffdir_parent,ffdir,STRLEN-1);
 546       p=strrchr(ffdir_parent,'/');
 547
 548       *p='\0';
 549
 550       fprintf(out,
 551               ";\tForce field data was read from:\n"
 552               ";\t%s\n"
 553               ";\n"
 554               ";\tNote:\n"
 555               ";\tThis might be a non-standard force field location. When you use this topology, the\n"
 556               ";\tforce field must either be present in the current directory, or the location\n"
 557               ";\tspecified in the GMXLIB path variable or with the 'include' mdp file option.\n;\n\n",
 558               ffdir_parent);
 559   }
 560 }
 561
 562 void print_top_header(FILE *out,const char *filename,
 563                       const char *title,gmx_bool bITP,const char *ffdir,real mHmult)
 564 {
 565     const char *p;
 566
 567     print_top_comment(out,filename,title,ffdir,bITP);
 568
 569     print_top_heavy_H(out, mHmult);
 570     fprintf(out,"; Include forcefield parameters\n");
 571
 572     p=strrchr(ffdir,'/');
 573     p = (ffdir[0]=='.' || p==NULL) ? ffdir : p+1;
 574
 575     fprintf(out,"#include \"%s/%s\"\n\n",p,fflib_forcefield_itp());
 576 }
 577
 578 static void print_top_posre(FILE *out,const char *pr)
 579 {
 580   fprintf(out,"; Include Position restraint file\n");
 581   fprintf(out,"#ifdef POSRES\n");
 582   fprintf(out,"#include \"%s\"\n",pr);
 583   fprintf(out,"#endif\n\n");
 584 }
 585
 586 static void print_top_water(FILE *out,const char *ffdir,const char *water)
 587 {
 588   const char *p;
 589   char  buf[STRLEN];
 590
 591   fprintf(out,"; Include water topology\n");
 592
 593   p=strrchr(ffdir,'/');
 594   p = (ffdir[0]=='.' || p==NULL) ? ffdir : p+1;
 595   fprintf(out,"#include \"%s/%s.itp\"\n",p,water);
 596
 597   fprintf(out,"\n");
 598   fprintf(out,"#ifdef POSRES_WATER\n");
 599   fprintf(out,"; Position restraint for each water oxygen\n");
 600   fprintf(out,"[ position_restraints ]\n");
 601   fprintf(out,";%3s %5s %9s %10s %10s\n","i","funct","fcx","fcy","fcz");
 602   fprintf(out,"%4d %4d %10g %10g %10g\n",1,1,1000.0,1000.0,1000.0);
 603   fprintf(out,"#endif\n");
 604   fprintf(out,"\n");
 605
 606   sprintf(buf,"%s/ions.itp",p);
 607
 608   if (fflib_fexist(buf))
 609   {
 610     fprintf(out,"; Include topology for ions\n");
 611     fprintf(out,"#include \"%s\"\n",buf);
 612     fprintf(out,"\n");
 613   }
 614 }
 615
 616 static void print_top_system(FILE *out, const char *title)
 617 {
 618   fprintf(out,"[ %s ]\n",dir2str(d_system));
 619   fprintf(out,"; Name\n");
 620   fprintf(out,"%s\n\n",title[0]?title:"Protein");
 621 }
 622
 623 void print_top_mols(FILE *out,
 624                     const char *title, const char *ffdir, const char *water,
 625                     int nincl, char **incls, int nmol, t_mols *mols)
 626 {
 627   int  i;
 628   char *incl;
 629
 630   if (nincl>0) {
 631     fprintf(out,"; Include chain topologies\n");
 632     for (i=0; (i<nincl); i++) {
 633         incl = strrchr(incls[i],DIR_SEPARATOR);
 634         if (incl == NULL) {
 635             incl = incls[i];
 636         } else {
 637             /* Remove the path from the include name */
 638             incl = incl + 1;
 639         }
 640       fprintf(out,"#include \"%s\"\n",incl);
 641     }
 642     fprintf(out,"\n");
 643   }
 644
 645     if (water)
 646     {
 647       print_top_water(out,ffdir,water);
 648     }
 649     print_top_system(out, title);
 650
 651   if (nmol) {
 652     fprintf(out,"[ %s ]\n",dir2str(d_molecules));
 653     fprintf(out,"; %-15s %5s\n","Compound","#mols");
 654     for (i=0; (i<nmol); i++)
 655       fprintf(out,"%-15s %5d\n",mols[i].name,mols[i].nr);
 656   }
 657 }
 658
 659 void write_top(FILE *out, char *pr,char *molname,
 660                t_atoms *at,gmx_bool bRTPresname,
 661                int bts[],t_params plist[],t_excls excls[],
 662                gpp_atomtype_t atype,int *cgnr, int nrexcl)
 663      /* NOTE: nrexcl is not the size of *excl! */
 664 {
 665   if (at && atype && cgnr) {
 666     fprintf(out,"[ %s ]\n",dir2str(d_moleculetype));
 667     fprintf(out,"; %-15s %5s\n","Name","nrexcl");
 668     fprintf(out,"%-15s %5d\n\n",molname?molname:"Protein",nrexcl);
 669
 670     print_atoms(out, atype, at, cgnr, bRTPresname);
 671     print_bondeds(out,at->nr,d_bonds,      F_BONDS,    bts[ebtsBONDS], plist);
 672     print_bondeds(out,at->nr,d_constraints,F_CONSTR,   0,              plist);
 673     print_bondeds(out,at->nr,d_constraints,F_CONSTRNC, 0,              plist);
 674     print_bondeds(out,at->nr,d_pairs,      F_LJ14,     0,              plist);
 675     print_excl(out,at->nr,excls);
 676     print_bondeds(out,at->nr,d_angles,     F_ANGLES,   bts[ebtsANGLES],plist);
 677     print_bondeds(out,at->nr,d_dihedrals,  F_PDIHS,    bts[ebtsPDIHS], plist);
 678     print_bondeds(out,at->nr,d_dihedrals,  F_IDIHS,    bts[ebtsIDIHS], plist);
 679     print_bondeds(out,at->nr,d_cmap,       F_CMAP,     bts[ebtsCMAP],  plist);
 680     print_bondeds(out,at->nr,d_polarization,F_POLARIZATION,   0,       plist);
 681     print_bondeds(out,at->nr,d_thole_polarization,F_THOLE_POL,0,       plist);
 682     print_bondeds(out,at->nr,d_vsites2,    F_VSITE2,   0,              plist);
 683     print_bondeds(out,at->nr,d_vsites3,    F_VSITE3,   0,              plist);
 684     print_bondeds(out,at->nr,d_vsites3,    F_VSITE3FD, 0,              plist);
 685     print_bondeds(out,at->nr,d_vsites3,    F_VSITE3FAD,0,              plist);
 686     print_bondeds(out,at->nr,d_vsites3,    F_VSITE3OUT,0,              plist);
 687     print_bondeds(out,at->nr,d_vsites4,    F_VSITE4FD, 0,              plist);
 688     print_bondeds(out,at->nr,d_vsites4,    F_VSITE4FDN, 0,             plist);
 689
 690     if (pr)
 691       print_top_posre(out,pr);
 692   }
 693 }
 694
 695 static atom_id search_res_atom(const char *type,int resind,
 696                                int natom,t_atom at[],
 697                                char ** const *aname,
 698                                const char *bondtype,gmx_bool bAllowMissing)
 699 {
 700   int i;
 701
 702   for(i=0; (i<natom); i++)
 703     if (at[i].resind == resind)
 704       return search_atom(type,i,natom,at,aname,bondtype,bAllowMissing);
 705
 706   return NO_ATID;
 707 }
 708
 709 static void do_ssbonds(t_params *ps,int natoms,t_atom atom[],char **aname[],
 710                        int nssbonds,t_ssbond *ssbonds,gmx_bool bAllowMissing)
 711 {
 712   int     i,ri,rj;
 713   atom_id ai,aj;
 714
 715   for(i=0; (i<nssbonds); i++) {
 716     ri = ssbonds[i].res1;
 717     rj = ssbonds[i].res2;
 718     ai = search_res_atom(ssbonds[i].a1,ri,natoms,atom,aname,
 719                          "special bond",bAllowMissing);
 720     aj = search_res_atom(ssbonds[i].a2,rj,natoms,atom,aname,
 721                          "special bond",bAllowMissing);
 722     if ((ai == NO_ATID) || (aj == NO_ATID))
 723       gmx_fatal(FARGS,"Trying to make impossible special bond (%s-%s)!",
 724                   ssbonds[i].a1,ssbonds[i].a2);
 725     add_param(ps,ai,aj,NULL,NULL);
 726   }
 727 }
 728
 729 static gmx_bool inter_res_bond(const t_rbonded *b)
 730 {
 731     return (b->AI[0] == '-' || b->AI[0] == '+' ||
 732             b->AJ[0] == '-' || b->AJ[0] == '+');
 733 }
 734
 735 static void at2bonds(t_params *psb, t_hackblock *hb,
 736                      int natoms, t_atom atom[], char **aname[],
 737                      int nres, rvec x[],
 738                      real long_bond_dist, real short_bond_dist,
 739                      gmx_bool bAllowMissing)
 740 {
 741   int     resind,i,j,k;
 742   atom_id ai,aj;
 743   real    dist2, long_bond_dist2, short_bond_dist2;
 744   const char *ptr;
 745
 746   long_bond_dist2  = sqr(long_bond_dist);
 747   short_bond_dist2 = sqr(short_bond_dist);
 748
 749   if (debug)
 750     ptr = "bond";
 751   else
 752     ptr = "check";
 753
 754   fprintf(stderr,"Making bonds...\n");
 755   i=0;
 756   for(resind=0; (resind < nres) && (i<natoms); resind++) {
 757     /* add bonds from list of bonded interactions */
 758     for(j=0; j < hb[resind].rb[ebtsBONDS].nb; j++) {
 759       /* Unfortunately we can not issue errors or warnings
 760        * for missing atoms in bonds, as the hydrogens and terminal atoms
 761        * have not been added yet.
 762        */
 763       ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,natoms,atom,aname,
 764                      ptr,TRUE);
 765       aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,natoms,atom,aname,
 766                      ptr,TRUE);
 767       if (ai != NO_ATID && aj != NO_ATID) {
 768           dist2 = distance2(x[ai],x[aj]);
 769           if (dist2 > long_bond_dist2 )
 770           {
 771               fprintf(stderr,"Warning: Long Bond (%d-%d = %g nm)\n",
 772                       ai+1,aj+1,sqrt(dist2));
 773           }
 774           else if (dist2 < short_bond_dist2 )
 775           {
 776               fprintf(stderr,"Warning: Short Bond (%d-%d = %g nm)\n",
 777                       ai+1,aj+1,sqrt(dist2));
 778           }
 779           add_param(psb,ai,aj,NULL,hb[resind].rb[ebtsBONDS].b[j].s);
 780       }
 781     }
 782     /* add bonds from list of hacks (each added atom gets a bond) */
 783     while( (i<natoms) && (atom[i].resind == resind) ) {
 784       for(j=0; j < hb[resind].nhack; j++)
 785         if ( ( hb[resind].hack[j].tp > 0 ||
 786                hb[resind].hack[j].oname==NULL ) &&
 787              strcmp(hb[resind].hack[j].AI,*(aname[i])) == 0 ) {
 788           switch(hb[resind].hack[j].tp) {
 789           case 9:          /* COOH terminus */
 790             add_param(psb,i,i+1,NULL,NULL);     /* C-O  */
 791             add_param(psb,i,i+2,NULL,NULL);     /* C-OA */
 792             add_param(psb,i+2,i+3,NULL,NULL);   /* OA-H */
 793             break;
 794           default:
 795             for(k=0; (k<hb[resind].hack[j].nr); k++)
 796               add_param(psb,i,i+k+1,NULL,NULL);
 797           }
 798         }
 799       i++;
 800     }
 801     /* we're now at the start of the next residue */
 802   }
 803 }
 804
 805 static int pcompar(const void *a, const void *b)
 806 {
 807   t_param *pa,*pb;
 808   int     d;
 809   pa=(t_param *)a;
 810   pb=(t_param *)b;
 811
 812   d = pa->AI - pb->AI;
 813   if (d == 0)
 814     d = pa->AJ - pb->AJ;
 815   if (d == 0)
 816     return strlen(pb->s) - strlen(pa->s);
 817   else
 818     return d;
 819 }
 820
 821 static void clean_bonds(t_params *ps)
 822 {
 823   int     i,j;
 824   atom_id a;
 825
 826   if (ps->nr > 0) {
 827     /* swap atomnumbers in bond if first larger than second: */
 828     for(i=0; (i<ps->nr); i++)
 829       if ( ps->param[i].AJ < ps->param[i].AI ) {
 830         a = ps->param[i].AI;
 831         ps->param[i].AI = ps->param[i].AJ;
 832         ps->param[i].AJ = a;
 833       }
 834
 835     /* Sort bonds */
 836     qsort(ps->param,ps->nr,(size_t)sizeof(ps->param[0]),pcompar);
 837
 838     /* remove doubles, keep the first one always. */
 839     j = 1;
 840     for(i=1; (i<ps->nr); i++) {
 841       if ((ps->param[i].AI != ps->param[j-1].AI) ||
 842           (ps->param[i].AJ != ps->param[j-1].AJ) ) {
 843         if (j != i) {
 844           cp_param(&(ps->param[j]),&(ps->param[i]));
 845         }
 846         j++;
 847       }
 848     }
 849     fprintf(stderr,"Number of bonds was %d, now %d\n",ps->nr,j);
 850     ps->nr=j;
 851   }
 852   else
 853     fprintf(stderr,"No bonds\n");
 854 }
 855
 856 void print_sums(t_atoms *atoms, gmx_bool bSystem)
 857 {
 858   double m,qtot;
 859   int    i;
 860   const char *where;
 861
 862   if (bSystem)
 863     where=" in system";
 864   else
 865     where="";
 866
 867   m=0;
 868   qtot=0;
 869   for(i=0; (i<atoms->nr); i++) {
 870     m+=atoms->atom[i].m;
 871     qtot+=atoms->atom[i].q;
 872   }
 873
 874   fprintf(stderr,"Total mass%s %.3f a.m.u.\n",where,m);
 875   fprintf(stderr,"Total charge%s %.3f e\n",where,qtot);
 876 }
 877
 878 static void check_restp_type(const char *name,int t1,int t2)
 879 {
 880     if (t1 != t2)
 881     {
 882         gmx_fatal(FARGS,"Residues in one molecule have a different '%s' type: %d and %d",name,t1,t2);
 883     }
 884 }
 885
 886 static void check_restp_types(t_restp *r0,t_restp *r1)
 887 {
 888     int i;
 889
 890     check_restp_type("all dihedrals",r0->bAlldih,r1->bAlldih);
 891     check_restp_type("nrexcl",r0->nrexcl,r1->nrexcl);
 892     check_restp_type("HH14",r0->HH14,r1->HH14);
 893     check_restp_type("remove dihedrals",r0->bRemoveDih,r1->bRemoveDih);
 894
 895     for(i=0; i<ebtsNR; i++)
 896     {
 897         check_restp_type(btsNames[i],r0->rb[i].type,r1->rb[i].type);
 898     }
 899 }
 900
 901 void add_atom_to_restp(t_restp *restp,int resnr,int at_start,const t_hack *hack)
 902 {
 903     char buf[STRLEN];
 904     int  k;
 905     const char *Hnum="123456";
 906
 907     /*if (debug)
 908     {
 909         fprintf(debug,"adding atom(s) %s to atom %s in res %d%s in rtp\n",
 910                 hack->nname,
 911                 *restp->atomname[at_start], resnr, restp->resname);
 912                 }*/
 913     strcpy(buf, hack->nname);
 914     buf[strlen(buf)+1]='\0';
 915     if ( hack->nr > 1 )
 916     {
 917         buf[strlen(buf)]='-';
 918     }
 919     /* make space */
 920     restp->natom += hack->nr;
 921     srenew(restp->atom,     restp->natom);
 922     srenew(restp->atomname, restp->natom);
 923     srenew(restp->cgnr,     restp->natom);
 924     /* shift the rest */
 925     for(k=restp->natom-1; k > at_start+hack->nr; k--)
 926     {
 927         restp->atom[k] =
 928             restp->atom    [k - hack->nr];
 929         restp->atomname[k] =
 930             restp->atomname[k - hack->nr];
 931         restp->cgnr[k] =
 932             restp->cgnr    [k - hack->nr];
 933     }
 934     /* now add them */
 935     for(k=0; k < hack->nr; k++)
 936     {
 937         /* set counter in atomname */
 938         if ( hack->nr > 1 )
 939         {
 940             buf[strlen(buf)-1] = Hnum[k];
 941         }
 942         snew( restp->atomname[at_start+1+k], 1);
 943         restp->atom     [at_start+1+k] = *hack->atom;
 944         *restp->atomname[at_start+1+k] = strdup(buf);
 945         if ( hack->cgnr != NOTSET )
 946         {
 947             restp->cgnr   [at_start+1+k] = hack->cgnr;
 948         }
 949         else
 950         {
 951             restp->cgnr   [at_start+1+k] = restp->cgnr[at_start];
 952         }
 953     }
 954 }
 955
 956 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
 957                                int nrtp, t_restp rtp[],
 958                                int nres, t_resinfo *resinfo,
 959                                int nterpairs,
 960                                t_hackblock **ntdb, t_hackblock **ctdb,
 961                                int *rn, int *rc)
 962 {
 963   int i, j, k, l;
 964   char *key;
 965   t_restp *res;
 966   char buf[STRLEN];
 967   const char *Hnum="123456";
 968   int tern,terc;
 969   gmx_bool bN,bC,bRM;
 970
 971   snew(*hb,nres);
 972   snew(*restp,nres);
 973   /* first the termini */
 974   for(i=0; i<nterpairs; i++) {
 975       if (rn[i] >= 0 && ntdb[i] != NULL) {
 976           copy_t_hackblock(ntdb[i], &(*hb)[rn[i]]);
 977       }
 978       if (rc[i] >= 0 && ctdb[i] != NULL) {
 979           merge_t_hackblock(ctdb[i], &(*hb)[rc[i]]);
 980       }
 981   }
 982
 983   /* then the whole rtp */
 984   for(i=0; i < nres; i++) {
 985     /* Here we allow a mismatch of one character when looking for the rtp entry.
 986      * For such a mismatch there should be only one mismatching name.
 987      * This is mainly useful for small molecules such as ions.
 988      * Note that this will usually not work for protein, DNA and RNA,
 989      * since there the residue names should be listed in residuetypes.dat
 990      * and an error will have been generated earlier in the process.
 991      */
 992     key = *resinfo[i].rtp;
 993     snew(resinfo[i].rtp,1);
 994     *resinfo[i].rtp = search_rtp(key,nrtp,rtp);
 995     res = get_restp(*resinfo[i].rtp,nrtp,rtp);
 996     copy_t_restp(res, &(*restp)[i]);
 997
 998     /* Check that we do not have different bonded types in one molecule */
 999     check_restp_types(&(*restp)[0],&(*restp)[i]);
1000
1001     tern = -1;
1002     for(j=0; j<nterpairs && tern==-1; j++) {
1003         if (i == rn[j]) {
1004             tern = j;
1005         }
1006     }
1007     terc = -1;
1008     for(j=0; j<nterpairs && terc == -1; j++) {
1009         if (i == rc[j]) {
1010             terc = j;
1011         }
1012     }
1013     bRM = merge_t_bondeds(res->rb, (*hb)[i].rb,tern>=0,terc>=0);
1014
1015     if (bRM && ((tern >= 0 && ntdb[tern] == NULL) ||
1016                 (terc >= 0 && ctdb[terc] == NULL))) {
1017         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.");
1018     }
1019     if (bRM && ((tern >= 0 && ntdb[tern]->nhack == 0) ||
1020                 (terc >= 0 && ctdb[terc]->nhack == 0))) {
1021         gmx_fatal(FARGS,"There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.");
1022     }
1023   }
1024
1025   /* now perform t_hack's on t_restp's,
1026      i.e. add's and deletes from termini database will be
1027      added to/removed from residue topology
1028      we'll do this on one big dirty loop, so it won't make easy reading! */
1029     for(i=0; i < nres; i++)
1030     {
1031         for(j=0; j < (*hb)[i].nhack; j++)
1032         {
1033             if ( (*hb)[i].hack[j].nr )
1034             {
1035                 /* find atom in restp */
1036                 for(l=0; l < (*restp)[i].natom; l++)
1037                     if ( ( (*hb)[i].hack[j].oname==NULL &&
1038                            strcmp((*hb)[i].hack[j].AI, *(*restp)[i].atomname[l])==0 ) ||
1039                          ( (*hb)[i].hack[j].oname!=NULL &&
1040                            strcmp((*hb)[i].hack[j].oname,*(*restp)[i].atomname[l])==0 ) )
1041                         break;
1042                 if (l == (*restp)[i].natom)
1043                 {
1044                     /* If we are doing an atom rename only, we don't need
1045                      * to generate a fatal error if the old name is not found
1046                      * in the rtp.
1047                      */
1048                     /* Deleting can happen also only on the input atoms,
1049                      * not necessarily always on the rtp entry.
1050                      */
1051                     if (!((*hb)[i].hack[j].oname != NULL &&
1052                           (*hb)[i].hack[j].nname != NULL) &&
1053                         !((*hb)[i].hack[j].oname != NULL &&
1054                           (*hb)[i].hack[j].nname == NULL))
1055                     {
1056                         gmx_fatal(FARGS,
1057                                   "atom %s not found in buiding block %d%s "
1058                                   "while combining tdb and rtp",
1059                                   (*hb)[i].hack[j].oname!=NULL ?
1060                                   (*hb)[i].hack[j].oname : (*hb)[i].hack[j].AI,
1061                                   i+1,*resinfo[i].rtp);
1062                     }
1063                 }
1064                 else
1065                 {
1066                     if ( (*hb)[i].hack[j].oname==NULL ) {
1067                         /* we're adding: */
1068                         add_atom_to_restp(&(*restp)[i],resinfo[i].nr,l,
1069                                           &(*hb)[i].hack[j]);
1070                     }
1071                     else
1072                     {
1073                         /* oname != NULL */
1074                         if ( (*hb)[i].hack[j].nname==NULL ) {
1075                             /* we're deleting */
1076                             if (debug)
1077                                 fprintf(debug, "deleting atom %s from res %d%s in rtp\n",
1078                                         *(*restp)[i].atomname[l],
1079                                         i+1,(*restp)[i].resname);
1080                             /* shift the rest */
1081                             (*restp)[i].natom--;
1082                             for(k=l; k < (*restp)[i].natom; k++) {
1083                                 (*restp)[i].atom    [k] = (*restp)[i].atom    [k+1];
1084                                 (*restp)[i].atomname[k] = (*restp)[i].atomname[k+1];
1085                                 (*restp)[i].cgnr    [k] = (*restp)[i].cgnr    [k+1];
1086                             }
1087                             /* give back space */
1088                             srenew((*restp)[i].atom,     (*restp)[i].natom);
1089                             srenew((*restp)[i].atomname, (*restp)[i].natom);
1090                             srenew((*restp)[i].cgnr,     (*restp)[i].natom);
1091                         } else { /* nname != NULL */
1092                             /* we're replacing */
1093                             if (debug)
1094                                 fprintf(debug, "replacing atom %s by %s in res %d%s in rtp\n",
1095                                         *(*restp)[i].atomname[l], (*hb)[i].hack[j].nname,
1096                                         i+1,(*restp)[i].resname);
1097                             snew( (*restp)[i].atomname[l], 1);
1098                             (*restp)[i].atom[l]      =       *(*hb)[i].hack[j].atom;
1099                             *(*restp)[i].atomname[l] = strdup((*hb)[i].hack[j].nname);
1100                             if ( (*hb)[i].hack[j].cgnr != NOTSET )
1101                                 (*restp)[i].cgnr   [l] = (*hb)[i].hack[j].cgnr;
1102                         }
1103                     }
1104                 }
1105             }
1106         }
1107     }
1108 }
1109
1110 static gmx_bool atomname_cmp_nr(const char *anm,t_hack *hack,int *nr)
1111 {
1112
1113     if (hack->nr == 1)
1114     {
1115         *nr = 0;
1116
1117         return (gmx_strcasecmp(anm,hack->nname) == 0);
1118     }
1119     else
1120     {
1121         if (isdigit(anm[strlen(anm)-1]))
1122         {
1123             *nr = anm[strlen(anm)-1] - '0';
1124         }
1125         else
1126         {
1127             *nr = 0;
1128         }
1129         if (*nr <= 0 || *nr > hack->nr)
1130         {
1131             return FALSE;
1132         }
1133         else
1134         {
1135             return (strlen(anm) == strlen(hack->nname) + 1 &&
1136                     gmx_strncasecmp(anm,hack->nname,strlen(hack->nname)) == 0);
1137         }
1138     }
1139 }
1140
1141 static gmx_bool match_atomnames_with_rtp_atom(t_atoms *pdba,rvec *x,int atind,
1142                                           t_restp *rptr,t_hackblock *hbr,
1143                                           gmx_bool bVerbose)
1144 {
1145     int  resnr;
1146     int  i,j,k;
1147     char *oldnm,*newnm;
1148     int  anmnr;
1149     char *start_at,buf[STRLEN];
1150     int  start_nr;
1151     gmx_bool bReplaceReplace,bFoundInAdd;
1152     gmx_bool bDeleted;
1153
1154     oldnm = *pdba->atomname[atind];
1155     resnr = pdba->resinfo[pdba->atom[atind].resind].nr;
1156
1157     bDeleted = FALSE;
1158     for(j=0; j<hbr->nhack; j++)
1159     {
1160         if (hbr->hack[j].oname != NULL && hbr->hack[j].nname != NULL &&
1161             gmx_strcasecmp(oldnm,hbr->hack[j].oname) == 0)
1162         {
1163             /* This is a replace entry. */
1164             /* Check if we are not replacing a replaced atom. */
1165             bReplaceReplace = FALSE;
1166             for(k=0; k<hbr->nhack; k++) {
1167                 if (k != j &&
1168                     hbr->hack[k].oname != NULL && hbr->hack[k].nname != NULL &&
1169                     gmx_strcasecmp(hbr->hack[k].nname,hbr->hack[j].oname) == 0)
1170                 {
1171                     /* The replace in hack[j] replaces an atom that
1172                      * was already replaced in hack[k], we do not want
1173                      * second or higher level replaces at this stage.
1174                      */
1175                     bReplaceReplace = TRUE;
1176                 }
1177             }
1178             if (bReplaceReplace)
1179             {
1180                 /* Skip this replace. */
1181                 continue;
1182             }
1183
1184             /* This atom still has the old name, rename it */
1185             newnm = hbr->hack[j].nname;
1186             for(k=0; k<rptr->natom; k++)
1187             {
1188                 if (gmx_strcasecmp(newnm,*rptr->atomname[k]) == 0)
1189                 {
1190                     break;
1191                 }
1192             }
1193             if (k == rptr->natom)
1194             {
1195                 /* The new name is not present in the rtp.
1196                  * We need to apply the replace also to the rtp entry.
1197                  */
1198
1199                 /* We need to find the add hack that can add this atom
1200                  * to find out after which atom it should be added.
1201                  */
1202                 bFoundInAdd = FALSE;
1203                 for(k=0; k<hbr->nhack; k++)
1204                 {
1205                     if (hbr->hack[k].oname == NULL &&
1206                         hbr->hack[k].nname != NULL &&
1207                         atomname_cmp_nr(newnm,&hbr->hack[k],&anmnr))
1208                     {
1209                         if (anmnr <= 1)
1210                         {
1211                             start_at = hbr->hack[k].a[0];
1212                         }
1213                         else
1214                         {
1215                             sprintf(buf,"%s%d",hbr->hack[k].nname,anmnr-1);
1216                             start_at = buf;
1217                         }
1218                         for(start_nr=0; start_nr<rptr->natom; start_nr++)
1219                         {
1220                             if (gmx_strcasecmp(start_at,(*rptr->atomname[start_nr])) == 0)
1221                             {
1222                                 break;
1223                             }
1224                         }
1225                         if (start_nr == rptr->natom)
1226                         {
1227                             gmx_fatal(FARGS,"Could not find atom '%s' in residue building block '%s' to add atom '%s' to",
1228                                       start_at,rptr->resname,newnm);
1229                         }
1230                         /* We can add the atom after atom start_nr */
1231                         add_atom_to_restp(rptr,resnr,start_nr,
1232                                           &hbr->hack[j]);
1233
1234                         bFoundInAdd = TRUE;
1235                     }
1236                 }
1237
1238                 if (!bFoundInAdd)
1239                 {
1240                     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'",
1241                               newnm,
1242                               hbr->hack[j].oname,hbr->hack[j].nname,
1243                               rptr->resname);
1244                 }
1245             }
1246
1247             if (bVerbose)
1248             {
1249                 printf("Renaming atom '%s' in residue '%s' %d to '%s'\n",
1250                        oldnm,rptr->resname,resnr,newnm);
1251             }
1252             /* Rename the atom in pdba */
1253             snew(pdba->atomname[atind],1);
1254             *pdba->atomname[atind] = strdup(newnm);
1255         }
1256         else if (hbr->hack[j].oname != NULL && hbr->hack[j].nname == NULL &&
1257                  gmx_strcasecmp(oldnm,hbr->hack[j].oname) == 0)
1258         {
1259             /* This is a delete entry, check if this atom is present
1260              * in the rtp entry of this residue.
1261              */
1262             for(k=0; k<rptr->natom; k++)
1263             {
1264                 if (gmx_strcasecmp(oldnm,*rptr->atomname[k]) == 0)
1265                 {
1266                     break;
1267                 }
1268             }
1269             if (k == rptr->natom)
1270             {
1271                 /* This atom is not present in the rtp entry,
1272                  * delete is now from the input pdba.
1273                  */
1274                 if (bVerbose)
1275                 {
1276                     printf("Deleting atom '%s' in residue '%s' %d\n",
1277                            oldnm,rptr->resname,resnr);
1278                 }
1279                 /* We should free the atom name,
1280                  * but it might be used multiple times in the symtab.
1281                  * sfree(pdba->atomname[atind]);
1282                  */
1283                 for(k=atind+1; k<pdba->nr; k++)
1284                 {
1285                     pdba->atom[k-1]     = pdba->atom[k];
1286                     pdba->atomname[k-1] = pdba->atomname[k];
1287                     copy_rvec(x[k],x[k-1]);
1288                 }
1289                 pdba->nr--;
1290                 bDeleted = TRUE;
1291             }
1292         }
1293     }
1294
1295     return bDeleted;
1296 }
1297
1298 void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
1299                               t_atoms *pdba,rvec *x,
1300                               gmx_bool bVerbose)
1301 {
1302     int  i,j,k;
1303     char *oldnm,*newnm;
1304     int  resnr;
1305     t_restp *rptr;
1306     t_hackblock *hbr;
1307     int  anmnr;
1308     char *start_at,buf[STRLEN];
1309     int  start_nr;
1310     gmx_bool bFoundInAdd;
1311
1312     for(i=0; i<pdba->nr; i++)
1313     {
1314         oldnm = *pdba->atomname[i];
1315         resnr = pdba->resinfo[pdba->atom[i].resind].nr;
1316         rptr  = &restp[pdba->atom[i].resind];
1317         for(j=0; (j<rptr->natom); j++)
1318         {
1319             if (gmx_strcasecmp(oldnm,*(rptr->atomname[j])) == 0)
1320             {
1321                 break;
1322             }
1323         }
1324         if (j == rptr->natom)
1325         {
1326             /* Not found yet, check if we have to rename this atom */
1327             if (match_atomnames_with_rtp_atom(pdba,x,i,
1328                                               rptr,&(hb[pdba->atom[i].resind]),
1329                                               bVerbose))
1330             {
1331                 /* We deleted this atom, decrease the atom counter by 1. */
1332                 i--;
1333             }
1334         }
1335     }
1336 }
1337
1338 void gen_cmap(t_params *psb, t_restp *restp, int natoms, t_atom atom[], char **aname[], int nres)
1339 {
1340         int     residx,i,ii,j,k;
1341         atom_id ai,aj,ak,al,am;
1342         const char *ptr;
1343
1344         if (debug)
1345                 ptr = "cmap";
1346         else
1347                 ptr = "check";
1348
1349         fprintf(stderr,"Making cmap torsions...");
1350         i=0;
1351         /* End loop at nres-1, since the very last residue does not have a +N atom, and
1352          * therefore we get a valgrind invalid 4 byte read error with atom am */
1353         for(residx=0; residx<nres-1; residx++)
1354         {
1355                 /* Add CMAP terms from the list of CMAP interactions */
1356                 for(j=0;j<restp[residx].rb[ebtsCMAP].nb; j++)
1357                 {
1358                         ai=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[0],i,natoms,atom,aname,
1359                                                    ptr,TRUE);
1360                         aj=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[1],i,natoms,atom,aname,
1361                                                    ptr,TRUE);
1362                         ak=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[2],i,natoms,atom,aname,
1363                                                    ptr,TRUE);
1364                         al=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[3],i,natoms,atom,aname,
1365                                                    ptr,TRUE);
1366                         am=search_atom(restp[residx].rb[ebtsCMAP].b[j].a[4],i,natoms,atom,aname,
1367                                                    ptr,TRUE);
1368
1369                         /* The first and last residues no not have cmap torsions */
1370                         if(ai!=NO_ATID && aj!=NO_ATID && ak!=NO_ATID && al!=NO_ATID && am!=NO_ATID)
1371                         {
1372                                 add_cmap_param(psb,ai,aj,ak,al,am,restp[residx].rb[ebtsCMAP].b[j].s);
1373                         }
1374                 }
1375
1376                 if(residx<nres-1)
1377                 {
1378                         while(atom[i].resind<residx+1)
1379                         {
1380                                 i++;
1381                         }
1382                 }
1383         }
1384
1385         /* Start the next residue */
1386 }
1387
1388 static void
1389 scrub_charge_groups(int *cgnr, int natoms)
1390 {
1391         int i;
1392
1393         for(i=0;i<natoms;i++)
1394         {
1395                 cgnr[i]=i+1;
1396         }
1397 }
1398
1399
1400 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
1401              t_atoms *atoms, rvec **x, gpp_atomtype_t atype, t_symtab *tab,
1402              int nrtp, t_restp rtp[],
1403              t_restp *restp, t_hackblock *hb,
1404              int nterpairs,t_hackblock **ntdb, t_hackblock **ctdb,
1405              gmx_bool bAllowMissing,
1406              gmx_bool bVsites, gmx_bool bVsiteAromatics,
1407              const char *ff, const char *ffdir,
1408              real mHmult,
1409              int nssbonds, t_ssbond *ssbonds,
1410              real long_bond_dist, real short_bond_dist,
1411              gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
1412              gmx_bool bRenumRes,gmx_bool bRTPresname)
1413 {
1414     /*
1415   t_hackblock *hb;
1416   t_restp  *restp;
1417     */
1418   t_params plist[F_NRE];
1419   t_excls  *excls;
1420   t_nextnb nnb;
1421   int      *cgnr;
1422   int      *vsite_type;
1423   int      i,nmissat;
1424   int      bts[ebtsNR];
1425
1426   init_plist(plist);
1427
1428   if (debug) {
1429     print_resall(debug, atoms->nres, restp, atype);
1430     dump_hb(debug, atoms->nres, hb);
1431   }
1432
1433   /* Make bonds */
1434   at2bonds(&(plist[F_BONDS]), hb,
1435            atoms->nr, atoms->atom, atoms->atomname, atoms->nres, *x,
1436            long_bond_dist, short_bond_dist, bAllowMissing);
1437
1438   /* specbonds: disulphide bonds & heme-his */
1439   do_ssbonds(&(plist[F_BONDS]),
1440              atoms->nr, atoms->atom, atoms->atomname, nssbonds, ssbonds,
1441              bAllowMissing);
1442
1443   nmissat = name2type(atoms, &cgnr, atype, restp);
1444   if (nmissat) {
1445     if (bAllowMissing)
1446       fprintf(stderr,"There were %d missing atoms in molecule %s\n",
1447               nmissat,molname);
1448     else
1449       gmx_fatal(FARGS,"There were %d missing atoms in molecule %s, if you want to use this incomplete topology anyhow, use the option -missing",
1450                   nmissat,molname);
1451   }
1452
1453   /* Cleanup bonds (sort and rm doubles) */
1454   clean_bonds(&(plist[F_BONDS]));
1455
1456   snew(vsite_type,atoms->nr);
1457   for(i=0; i<atoms->nr; i++)
1458     vsite_type[i]=NOTSET;
1459   if (bVsites) {
1460     /* determine which atoms will be vsites and add dummy masses
1461        also renumber atom numbers in plist[0..F_NRE]! */
1462     do_vsites(nrtp, rtp, atype, atoms, tab, x, plist,
1463               &vsite_type, &cgnr, mHmult, bVsiteAromatics, ffdir);
1464   }
1465
1466   /* Make Angles and Dihedrals */
1467   fprintf(stderr,"Generating angles, dihedrals and pairs...\n");
1468   snew(excls,atoms->nr);
1469   init_nnb(&nnb,atoms->nr,4);
1470   gen_nnb(&nnb,plist);
1471   print_nnb(&nnb,"NNB");
1472   gen_pad(&nnb,atoms,restp[0].nrexcl,restp[0].HH14,
1473           plist,excls,hb,restp[0].bAlldih,restp[0].bRemoveDih,
1474           bAllowMissing);
1475   done_nnb(&nnb);
1476
1477     /* Make CMAP */
1478     if (TRUE == bCmap)
1479     {
1480                 gen_cmap(&(plist[F_CMAP]), restp, atoms->nr, atoms->atom, atoms->atomname, atoms->nres);
1481         if (plist[F_CMAP].nr > 0)
1482         {
1483             fprintf(stderr, "There are %4d cmap torsion pairs\n",
1484                     plist[F_CMAP].nr);
1485         }
1486     }
1487
1488   /* set mass of all remaining hydrogen atoms */
1489   if (mHmult != 1.0)
1490     do_h_mass(&(plist[F_BONDS]),vsite_type,atoms,mHmult,bDeuterate);
1491   sfree(vsite_type);
1492
1493   /* Cleanup bonds (sort and rm doubles) */
1494   /* clean_bonds(&(plist[F_BONDS]));*/
1495
1496   fprintf(stderr,
1497           "There are %4d dihedrals, %4d impropers, %4d angles\n"
1498           "          %4d pairs,     %4d bonds and  %4d virtual sites\n",
1499           plist[F_PDIHS].nr, plist[F_IDIHS].nr, plist[F_ANGLES].nr,
1500           plist[F_LJ14].nr, plist[F_BONDS].nr,
1501           plist[F_VSITE2].nr +
1502           plist[F_VSITE3].nr +
1503           plist[F_VSITE3FD].nr +
1504           plist[F_VSITE3FAD].nr +
1505           plist[F_VSITE3OUT].nr +
1506       plist[F_VSITE4FD].nr +
1507       plist[F_VSITE4FDN].nr );
1508
1509   print_sums(atoms, FALSE);
1510
1511   if (FALSE == bChargeGroups)
1512   {
1513           scrub_charge_groups(cgnr, atoms->nr);
1514   }
1515
1516     if (bRenumRes)
1517     {
1518         for(i=0; i<atoms->nres; i++)
1519         {
1520             atoms->resinfo[i].nr = i + 1;
1521             atoms->resinfo[i].ic = ' ';
1522         }
1523     }
1524
1525   if (top_file) {
1526     fprintf(stderr,"Writing topology\n");
1527     /* We can copy the bonded types from the first restp,
1528      * since the types have to be identical for all residues in one molecule.
1529      */
1530     for(i=0; i<ebtsNR; i++) {
1531         bts[i] = restp[0].rb[i].type;
1532     }
1533     write_top(top_file, posre_fn, molname,
1534               atoms, bRTPresname,
1535               bts, plist, excls, atype, cgnr, restp[0].nrexcl);
1536   }
1537
1538   /* cleaning up */
1539   free_t_hackblock(atoms->nres, &hb);
1540   free_t_restp(atoms->nres, &restp);
1541
1542   /* we should clean up hb and restp here, but that is a *L*O*T* of work! */
1543   sfree(cgnr);
1544   for (i=0; i<F_NRE; i++)
1545     sfree(plist[i].param);
1546   for (i=0; i<atoms->nr; i++)
1547     sfree(excls[i].e);
1548   sfree(excls);
1549 }