OpenMM: added combination rule check, disabled restraint check for now as it's buggy

[gromacs/qmmm-gamess-us.git] / src / kernel / x2top.c

/*
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.3.3
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2008, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * For more info, check our website at http://www.gromacs.org
 * 
 * And Hey:
 * Groningen Machine for Chemical Simulation
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "maths.h"
#include "macros.h"
#include "copyrite.h"
#include "bondf.h"
#include "gmxfio.h"
#include "string2.h"
#include "smalloc.h"
#include "strdb.h"
#include "sysstuff.h"
#include "confio.h"
#include "physics.h"
#include "statutil.h"
#include "vec.h"
#include "random.h"
#include "3dview.h"
#include "txtdump.h"
#include "readinp.h"
#include "names.h"
#include "toppush.h"
#include "pdb2top.h"
#include "gen_ad.h"
#include "gpp_nextnb.h"
#include "vec.h"
#include "x2top.h"
#include "atomprop.h"

char atp[7] = "HCNOSX";
#define NATP (asize(atp)-1)

real blen[NATP][NATP] = { 
  {  0.00,  0.108, 0.105, 0.10, 0.10, 0.10 },
  {  0.108, 0.15,  0.14,  0.14, 0.16, 0.14 },
  {  0.105, 0.14,  0.14,  0.14, 0.16, 0.14 },
  {  0.10,  0.14,  0.14,  0.14, 0.17, 0.14 },
  {  0.10,  0.16,  0.16,  0.17, 0.20, 0.17 },
  {  0.10,  0.14,  0.14,  0.14, 0.17, 0.17 }
};

#define MARGIN_FAC 1.1

static real set_x_blen(real scale)
{
  real maxlen;
  int  i,j;

  for(i=0; i<NATP-1; i++) {
    blen[NATP-1][i] *= scale;
    blen[i][NATP-1] *= scale;
  }
  blen[NATP-1][NATP-1] *= scale;
  
  maxlen = 0;
  for(i=0; i<NATP; i++)
    for(j=0; j<NATP; j++)
      if (blen[i][j] > maxlen)
        maxlen = blen[i][j];
  
  return maxlen*MARGIN_FAC;
}

static bool is_bond(int nnm,t_nm2type nmt[],char *ai,char *aj,real blen)
{
  int i,j;
    
  for(i=0; (i<nnm); i++) {
    for(j=0; (j<nmt[i].nbonds); j++) {
      if ((((strncasecmp(ai,nmt[i].elem,1) == 0) && 
           (strncasecmp(aj,nmt[i].bond[j],1) == 0)) ||
          ((strncasecmp(ai,nmt[i].bond[j],1) == 0) && 
           (strncasecmp(aj,nmt[i].elem,1) == 0))) &&
          (fabs(blen-nmt[i].blen[j]) <= 0.1*nmt[i].blen[j]))
        return TRUE;
    }
  }
  return FALSE;
}

static int get_atype(char *nm)
{
  int i,aai=NATP-1;
  
  for(i=0; (i<NATP-1); i++) {
    if (nm[0] == atp[i]) {
      aai=i;
      break;
    }
  }
  return aai;
}

void mk_bonds(int nnm,t_nm2type nmt[],
              t_atoms *atoms,rvec x[],t_params *bond,int nbond[],char *ff,
              bool bPBC,matrix box,gmx_atomprop_t aps)
{
  t_param b;
  int     i,j;
  t_pbc   pbc;
  rvec    dx;
  real    dx2;
  
  for(i=0; (i<MAXATOMLIST); i++)
    b.a[i] = -1;
  for(i=0; (i<MAXFORCEPARAM); i++)
    b.c[i] = 0.0;
    
  if (bPBC)
    set_pbc(&pbc,epbcXYZ,box);
  for(i=0; (i<atoms->nr); i++) {
    if ((i % 10) == 0)
      fprintf(stderr,"\ratom %d",i);
    for(j=i+1; (j<atoms->nr); j++) {
      if (bPBC)
        pbc_dx(&pbc,x[i],x[j],dx);
      else
        rvec_sub(x[i],x[j],dx);
      
      dx2 = iprod(dx,dx);
      if (is_bond(nnm,nmt,*atoms->atomname[i],*atoms->atomname[j],
                  sqrt(dx2))) {
        b.AI = i;
        b.AJ = j;
        b.C0 = sqrt(dx2);
        add_param_to_list (bond,&b);
        nbond[i]++;
        nbond[j]++;
        if (debug) 
          fprintf(debug,"Bonding atoms %s-%d and %s-%d\n",
                  *atoms->atomname[i],i+1,*atoms->atomname[j],j+1);
      }
    }
  }
  fprintf(stderr,"\ratom %d\n",i);
}

int *set_cgnr(t_atoms *atoms,bool bUsePDBcharge,real *qtot,real *mtot)
{
  int    i,n=1;
  int    *cgnr;
  double qt=0,mt=0;
  
  *qtot = *mtot = 0;
  snew(cgnr,atoms->nr);
  for(i=0; (i<atoms->nr); i++) {
    if (atoms->pdbinfo && bUsePDBcharge)
      atoms->atom[i].q = atoms->pdbinfo[i].bfac;
    qt += atoms->atom[i].q;
    *qtot += atoms->atom[i].q;
    *mtot += atoms->atom[i].m;
    cgnr[i] = n;
    if (is_int(qt)) {
      n++;
      qt=0;
    }
  }
  return cgnr;
}

gpp_atomtype_t set_atom_type(t_symtab *tab,t_atoms *atoms,t_params *bonds,
                             int *nbonds,int nnm,t_nm2type nm2t[])
{
  gpp_atomtype_t atype;
  int nresolved;
  
  atype = init_atomtype();
  snew(atoms->atomtype,atoms->nr);
  nresolved = nm2type(nnm,nm2t,tab,atoms,atype,nbonds,bonds);
  if (nresolved != atoms->nr)
    gmx_fatal(FARGS,"Could only find a forcefield type for %d out of %d atoms",
              nresolved,atoms->nr);
  
  fprintf(stderr,"There are %d different atom types in your sample\n",
          get_atomtype_ntypes(atype));
  
  return atype;
}

void lo_set_force_const(t_params *plist,real c[],int nrfp,bool bRound,
                        bool bDih,bool bParam)
{
  int    i,j;
  double cc;
  char   buf[32];
  
  for(i=0; (i<plist->nr); i++) {
    if (!bParam)
      for(j=0; j<nrfp; j++)
        c[j] = NOTSET;
    else {
      if (bRound) {
        sprintf(buf,"%.2e",plist->param[i].c[0]);
        sscanf(buf,"%lf",&cc);
        c[0] = cc;
      }
      else 
        c[0] = plist->param[i].c[0];
      if (bDih) {
        c[0] *= c[2];
        c[0] = ((int)(c[0] + 3600)) % 360;
        if (c[0] > 180)
          c[0] -= 360;
        /* To put the minimum at the current angle rather than the maximum */
        c[0] += 180; 
      }
    }
    for(j=0; (j<nrfp); j++) {
      plist->param[i].c[j]      = c[j];
      plist->param[i].c[nrfp+j] = c[j];
    }
    set_p_string(&(plist->param[i]),"");
  }
}

void set_force_const(t_params plist[],real kb,real kt,real kp,bool bRound,
                     bool bParam)
{
  int i;
  real c[MAXFORCEPARAM];
  
  c[0] = 0;
  c[1] = kb;
  lo_set_force_const(&plist[F_BONDS],c,2,bRound,FALSE,bParam);
  c[1] = kt;
  lo_set_force_const(&plist[F_ANGLES],c,2,bRound,FALSE,bParam);
  c[1] = kp;
  c[2] = 3;
  lo_set_force_const(&plist[F_PDIHS],c,3,bRound,TRUE,bParam);
}

void calc_angles_dihs(t_params *ang,t_params *dih,rvec x[],bool bPBC,
                      matrix box)
{
  int    i,ai,aj,ak,al,t1,t2,t3;
  rvec   r_ij,r_kj,r_kl,m,n;
  real   sign,th,costh,ph;
  t_pbc  pbc;

  if (bPBC)
    set_pbc(&pbc,epbcXYZ,box);
  if (debug)
    pr_rvecs(debug,0,"X2TOP",box,DIM);
  for(i=0; (i<ang->nr); i++) {
    ai = ang->param[i].AI;
    aj = ang->param[i].AJ;
    ak = ang->param[i].AK;
    th = RAD2DEG*bond_angle(x[ai],x[aj],x[ak],bPBC ? &pbc : NULL,
                            r_ij,r_kj,&costh,&t1,&t2);
    if (debug)
      fprintf(debug,"X2TOP: ai=%3d aj=%3d ak=%3d r_ij=%8.3f r_kj=%8.3f th=%8.3f\n",
              ai,aj,ak,norm(r_ij),norm(r_kj),th);
    ang->param[i].C0 = th;
  }
  for(i=0; (i<dih->nr); i++) {
    ai = dih->param[i].AI;
    aj = dih->param[i].AJ;
    ak = dih->param[i].AK;
    al = dih->param[i].AL;
    ph = RAD2DEG*dih_angle(x[ai],x[aj],x[ak],x[al],bPBC ? & pbc : NULL,
                           r_ij,r_kj,r_kl,m,n,&sign,&t1,&t2,&t3);
    if (debug)
      fprintf(debug,"X2TOP: ai=%3d aj=%3d ak=%3d al=%3d r_ij=%8.3f r_kj=%8.3f r_kl=%8.3f ph=%8.3f\n",
              ai,aj,ak,al,norm(r_ij),norm(r_kj),norm(r_kl),ph);
    dih->param[i].C0 = ph;
  }
}

static void dump_hybridization(FILE *fp,t_atoms *atoms,int nbonds[])
{
  int i;
  
  for(i=0; (i<atoms->nr); i++) {
    fprintf(fp,"Atom %5s has %1d bonds\n",*atoms->atomname[i],nbonds[i]);
  }
}

static void print_pl(FILE *fp,t_params plist[],int ftp,const char *name,
                     char ***atomname)
{ 
  int i,j,nral,nrfp;

  if (plist[ftp].nr > 0) {
    fprintf(fp,"\n");
    fprintf(fp,"[ %s ]\n",name);
    nral = interaction_function[ftp].nratoms;
    nrfp = interaction_function[ftp].nrfpA;
    for(i=0; (i<plist[ftp].nr); i++) {
      for(j=0; (j<nral); j++) 
        fprintf(fp,"  %5s",*atomname[plist[ftp].param[i].a[j]]);
      for(j=0; (j<nrfp); j++) {
        if (plist[ftp].param[i].c[j] != NOTSET)
          fprintf(fp,"  %10.3e",plist[ftp].param[i].c[j]);
      }
      fprintf(fp,"\n");
    }
  }
}

static void print_rtp(const char *filenm,const char *title,t_atoms *atoms,
                      t_params plist[],gpp_atomtype_t atype,int cgnr[],
                      int nbts,int bts[])
{
  FILE *fp;
  int i,tp;
  char *tpnm;

  fp = gmx_fio_fopen(filenm,"w");
  fprintf(fp,"; %s\n",title);
  fprintf(fp,"\n");
  fprintf(fp,"[ %s ]\n",*atoms->resinfo[0].name);
  fprintf(fp,"\n");
  fprintf(fp,"[ atoms ]\n");
  for(i=0; (i<atoms->nr); i++) {
    tp = atoms->atom[i].type;
    if ((tpnm = get_atomtype_name(tp,atype)) == NULL)
      gmx_fatal(FARGS,"tp = %d, i = %d in print_rtp",tp,i);
    fprintf(fp,"%-8s  %12s  %8.4f  %5d\n",
            *atoms->atomname[i],tpnm,
            atoms->atom[i].q,cgnr[i]);
  }
  print_pl(fp,plist,F_BONDS,"bonds",atoms->atomname);
  print_pl(fp,plist,F_ANGLES,"angles",atoms->atomname);
  print_pl(fp,plist,F_PDIHS,"dihedrals",atoms->atomname);
  print_pl(fp,plist,F_IDIHS,"impropers",atoms->atomname);
  
  gmx_fio_fclose(fp);
}

int main(int argc, char *argv[])
{
  const char *desc[] = {
    "x2top generates a primitive topology from a coordinate file.",
    "The program assumes all hydrogens are present when defining",
    "the hybridization from the atom name and the number of bonds.",
    "The program can also make an rtp entry, which you can then add",
    "to the rtp database.[PAR]",
    "When [TT]-param[tt] is set, equilibrium distances and angles",
    "and force constants will be printed in the topology for all",
    "interactions. The equilibrium distances and angles are taken",
    "from the input coordinates, the force constant are set with",
    "command line options."
    "The force fields supported currently are:[PAR]",
    "G43a1  GROMOS96 43a1 Forcefield (official distribution)[PAR]",
    "oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)[PAR]",
    "G43b1  GROMOS96 43b1 Vacuum Forcefield (official distribution)[PAR]",
    "gmx    Gromacs Forcefield (a modified GROMOS87, see manual)[PAR]",
    "G43a2  GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)[PAR]",
    "The corresponding data files can be found in the library directory",
    "with names like ffXXXX.YYY. Check chapter 5 of the manual for more",
    "information about file formats. By default the forcefield selection",
    "is interactive, but you can use the [TT]-ff[tt] option to specify",
    "one of the short names above on the command line instead. In that",
    "case pdb2gmx just looks for the corresponding file.[PAR]",
  };
  const char *bugs[] = {
    "The atom type selection is primitive. Virtually no chemical knowledge is used",
    "Periodic boundary conditions screw up the bonding",
    "No improper dihedrals are generated",
    "The atoms to atomtype translation table is incomplete (ffG43a1.n2t file in the $GMXLIB directory). Please extend it and send the results back to the GROMACS crew."
  };
  FILE       *fp;
  t_params   plist[F_NRE];
  t_excls    *excls;
  t_atoms    *atoms;       /* list with all atoms */
  gpp_atomtype_t atype;
  t_nextnb   nnb;
  t_nm2type  *nm2t;
  t_mols     mymol;
  gmx_atomprop_t aps;
  int        nnm;
  char       title[STRLEN],forcefield[32],ffdir[STRLEN];
  rvec       *x;        /* coordinates? */
  int        *nbonds,*cgnr;
  int        bts[] = { 1,1,1,2 };
  matrix     box;          /* box length matrix */
  int        natoms;       /* number of atoms in one molecule  */
  int        nres;         /* number of molecules? */
  int        i,j,k,l,m,ndih;
  int        epbc;
  bool       bRTP,bTOP,bOPLS;
  t_symtab   symtab;
  real       cutoff,qtot,mtot;
  output_env_t oenv;
  
  t_filenm fnm[] = {
    { efSTX, "-f", "conf", ffREAD  },
    { efTOP, "-o", "out",  ffOPTWR },
    { efRTP, "-r", "out",  ffOPTWR }
  };
#define NFILE asize(fnm)
  static real scale = 1.1, kb = 4e5,kt = 400,kp = 5;
  static int  nexcl = 3;
  static bool bRemoveDih = FALSE;
  static bool bParam = TRUE, bH14 = TRUE,bAllDih = FALSE,bRound = TRUE;
  static bool bPairs = TRUE, bPBC = TRUE;
  static bool bUsePDBcharge = FALSE,bVerbose=FALSE;
  static const char *molnm = "ICE";
  static const char *ff = "oplsaa";
  t_pargs pa[] = {
    { "-ff",     FALSE, etSTR, {&ff},
      "Force field for your simulation. Type \"select\" for interactive selcection." },
    { "-v",      FALSE, etBOOL, {&bVerbose},
      "Generate verbose output in the top file." },
    { "-nexcl", FALSE, etINT,  {&nexcl},
      "Number of exclusions" },
    { "-H14",    FALSE, etBOOL, {&bH14}, 
      "Use 3rd neighbour interactions for hydrogen atoms" },
    { "-alldih", FALSE, etBOOL, {&bAllDih}, 
      "Generate all proper dihedrals" },
    { "-remdih", FALSE, etBOOL, {&bRemoveDih}, 
      "Remove dihedrals on the same bond as an improper" },
    { "-pairs",  FALSE, etBOOL, {&bPairs},
      "Output 1-4 interactions (pairs) in topology file" },
    { "-name",   FALSE, etSTR,  {&molnm},
      "Name of your molecule" },
    { "-pbc",    FALSE, etBOOL, {&bPBC},
      "Use periodic boundary conditions." },
    { "-pdbq",  FALSE, etBOOL, {&bUsePDBcharge},
      "Use the B-factor supplied in a pdb file for the atomic charges" },
    { "-param", FALSE, etBOOL, {&bParam},
      "Print parameters in the output" },
    { "-round",  FALSE, etBOOL, {&bRound},
      "Round off measured values" },
    { "-kb",    FALSE, etREAL, {&kb},
      "Bonded force constant (kJ/mol/nm^2)" },
    { "-kt",    FALSE, etREAL, {&kt},
      "Angle force constant (kJ/mol/rad^2)" },
    { "-kp",    FALSE, etREAL, {&kp},
      "Dihedral angle force constant (kJ/mol/rad^2)" }
  };
  
  CopyRight(stdout,argv[0]);

  parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
                    asize(desc),desc,asize(bugs),bugs,&oenv);
  bRTP = opt2bSet("-r",NFILE,fnm);
  bTOP = opt2bSet("-o",NFILE,fnm);
  
  if (!bRTP && !bTOP)
    gmx_fatal(FARGS,"Specify at least one output file");

  aps = gmx_atomprop_init();
    
  /* Force field selection, interactive or direct */
  choose_ff(strcmp(ff,"select") == 0 ? NULL : ff,
            forcefield,sizeof(forcefield),
            ffdir,sizeof(ffdir));

  bOPLS = (strcmp(forcefield,"ffoplsaa") == 0);
  
    
  mymol.name = strdup(molnm);
  mymol.nr   = 1;
        
  /* Init parameter lists */
  init_plist(plist);
  
  /* Read coordinates */
  get_stx_coordnum(opt2fn("-f",NFILE,fnm),&natoms); 
  snew(atoms,1);
  
  /* make space for all the atoms */
  init_t_atoms(atoms,natoms,TRUE);
  snew(x,natoms);              

  read_stx_conf(opt2fn("-f",NFILE,fnm),title,atoms,x,NULL,&epbc,box);

  nm2t = rd_nm2type(ffdir,&nnm);
  printf("There are %d name to type translations\n",nnm);
  if (debug)
    dump_nm2type(debug,nnm,nm2t);
  
  printf("Generating bonds from distances...\n");
  snew(nbonds,atoms->nr);
  mk_bonds(nnm,nm2t,atoms,x,&(plist[F_BONDS]),nbonds,forcefield,
           bPBC,box,aps);

  open_symtab(&symtab);
  atype = set_atom_type(&symtab,atoms,&(plist[F_BONDS]),nbonds,nnm,nm2t);
  
  /* Make Angles and Dihedrals */
  snew(excls,atoms->nr);
  printf("Generating angles and dihedrals from bonds...\n");
  init_nnb(&nnb,atoms->nr,4);
  gen_nnb(&nnb,plist);
  print_nnb(&nnb,"NNB");
  gen_pad(&nnb,atoms,bH14,nexcl,plist,excls,NULL,bAllDih,bRemoveDih,TRUE);
  done_nnb(&nnb);

  if (!bPairs)
    plist[F_LJ14].nr = 0;
  fprintf(stderr,
          "There are %4d %s dihedrals, %4d impropers, %4d angles\n"
          "          %4d pairs,     %4d bonds and  %4d atoms\n",
          plist[F_PDIHS].nr, 
          bOPLS ? "Ryckaert-Bellemans" : "proper",
          plist[F_IDIHS].nr, plist[F_ANGLES].nr,
          plist[F_LJ14].nr, plist[F_BONDS].nr,atoms->nr);

  calc_angles_dihs(&plist[F_ANGLES],&plist[F_PDIHS],x,bPBC,box);
  
  set_force_const(plist,kb,kt,kp,bRound,bParam);

  cgnr = set_cgnr(atoms,bUsePDBcharge,&qtot,&mtot);
  printf("Total charge is %g, total mass is %g\n",qtot,mtot);
  if (bOPLS) {
    bts[2] = 3;
    bts[3] = 1;
  }
  
  if (bTOP) {    
    fp = ftp2FILE(efTOP,NFILE,fnm,"w");
    print_top_header(fp,ftp2fn(efTOP,NFILE,fnm),
                     "Generated by x2top",TRUE,ffdir,1.0);
    
    write_top(fp,NULL,mymol.name,atoms,FALSE,bts,plist,excls,atype,
              cgnr,nexcl);
    print_top_mols(fp,mymol.name,ffdir,NULL,0,NULL,1,&mymol);
    
    ffclose(fp);
  }
  if (bRTP)
    print_rtp(ftp2fn(efRTP,NFILE,fnm),"Generated by x2top",
              atoms,plist,atype,cgnr,asize(bts),bts);
  
  if (debug) {
    dump_hybridization(debug,atoms,nbonds);
  }
  close_symtab(&symtab);

  printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",Program());
  printf("         Please verify atomtypes and charges by comparison to other\n");
  printf("         topologies.\n");
      
  thanx(stderr);
  
  return 0;
}