static void print_rtp(const char *filenm, const char *title, t_atoms *atoms,
t_params plist[], gpp_atomtype_t atype, int cgnr[])
{
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);
}
static void print_resatoms(FILE *out,gpp_atomtype_t atype,t_restp *rtp)
{
int j,tp;
char *tpnm;
/* fprintf(out,"%5s\n",rtp->resname);
fprintf(out,"%5d\n",rtp->natom); */
fprintf(out,"[ %s ]\n",rtp->resname);
fprintf(out," [ atoms ]\n");
for(j=0; (j<rtp->natom); j++) {
tp = rtp->atom[j].type;
tpnm = get_atomtype_name(tp,atype);
if (tpnm == NULL)
gmx_fatal(FARGS,"Incorrect atomtype (%d)",tp);
fprintf(out,"%6s %6s %8.3f %6d\n",
*(rtp->atomname[j]),tpnm,rtp->atom[j].q,rtp->cgnr[j]);
}
}
static void print_atom(FILE *out,t_atom *a,gpp_atomtype_t atype,char *newnm)
{
fprintf(out,"\t%s\t%g\t%g\n",
get_atomtype_name(a->type,atype),a->m,a->q);
}
void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
gmx_bool bRTPresname)
{
int i, ri;
int tpA, tpB;
const char *as;
char *tpnmA, *tpnmB;
double qres, qtot;
as = dir2str(d_atoms);
fprintf(out, "[ %s ]\n", as);
fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
"nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
qtot = 0;
if (debug)
{
fprintf(debug, "This molecule has %d atoms and %d residues\n",
at->nr, at->nres);
}
if (at->nres)
{
/* if the information is present... */
for (i = 0; (i < at->nr); i++)
{
ri = at->atom[i].resind;
if ((i == 0 || ri != at->atom[i-1].resind) &&
at->resinfo[ri].rtp != NULL)
{
qres = get_residue_charge(at, i);
fprintf(out, "; residue %3d %-3s rtp %-4s q ",
at->resinfo[ri].nr,
*at->resinfo[ri].name,
*at->resinfo[ri].rtp);
if (fabs(qres) < 0.001)
{
fprintf(out, " %s", "0.0");
}
else
{
fprintf(out, "%+3.1f", qres);
}
fprintf(out, "\n");
}
tpA = at->atom[i].type;
if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
{
gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
}
fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
i+1, tpnmA,
at->resinfo[ri].nr,
at->resinfo[ri].ic,
bRTPresname ?
*(at->resinfo[at->atom[i].resind].rtp) :
*(at->resinfo[at->atom[i].resind].name),
*(at->atomname[i]), cgnr[i],
at->atom[i].q, at->atom[i].m);
if (PERTURBED(at->atom[i]))
{
tpB = at->atom[i].typeB;
if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
{
gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
}
fprintf(out, " %6s %10g %10g",
tpnmB, at->atom[i].qB, at->atom[i].mB);
}
qtot += (double)at->atom[i].q;
if (fabs(qtot) < 4*GMX_REAL_EPS)
{
qtot = 0;
}
fprintf(out, " ; qtot %.4g\n", qtot);
}
}
fprintf(out, "\n");
fflush(out);
}
void print_bt(FILE *out, directive d, gpp_atomtype_t at,
int ftype, int fsubtype, t_params plist[],
gmx_bool bFullDih)
{
/* This dihp is a DIRTY patch because the dih-types do not use
* all four atoms to determine the type.
*/
const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
t_params *bt;
int i, j, f, nral, nrfp;
gmx_bool bDih = FALSE, bSwapParity;
bt = &(plist[ftype]);
if (!bt->nr)
{
return;
}
f = 0;
switch (ftype)
{
case F_G96ANGLES:
f = 1;
break;
case F_G96BONDS:
f = 1;
break;
case F_MORSE:
f = 2;
break;
case F_CUBICBONDS:
f = 3;
break;
case F_CONNBONDS:
f = 4;
break;
case F_HARMONIC:
f = 5;
break;
case F_CROSS_BOND_ANGLES:
f = 2;
break;
case F_CROSS_BOND_BONDS:
f = 3;
break;
case F_UREY_BRADLEY:
f = 4;
break;
case F_PDIHS:
case F_RBDIHS:
case F_FOURDIHS:
bDih = TRUE;
break;
case F_IDIHS:
f = 1;
bDih = TRUE;
break;
case F_CONSTRNC:
f = 1;
break;
case F_VSITE3FD:
f = 1;
break;
case F_VSITE3FAD:
f = 2;
break;
case F_VSITE3OUT:
f = 3;
break;
case F_VSITE4FDN:
f = 1;
break;
case F_CMAP:
f = 1;
break;
default:
bDih = FALSE;
}
if (bFullDih)
{
bDih = FALSE;
}
if (fsubtype)
{
f = fsubtype-1;
}
nral = NRAL(ftype);
nrfp = NRFP(ftype);
/* header */
fprintf(out, "[ %s ]\n", dir2str(d));
fprintf(out, "; ");
if (!bDih)
{
fprintf (out, "%3s %4s", "ai", "aj");
for (j = 2; (j < nral); j++)
{
fprintf (out, " %3c%c", 'a', 'i'+j);
}
}
else
{
for (j = 0; (j < 2); j++)
{
fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
}
}
fprintf (out, " funct");
for (j = 0; (j < nrfp); j++)
{
fprintf (out, " %12c%1d", 'c', j);
}
fprintf (out, "\n");
/* print bondtypes */
for (i = 0; (i < bt->nr); i++)
{
bSwapParity = (bt->param[i].C0 == NOTSET) && (bt->param[i].C1 == -1);
if (!bDih)
{
for (j = 0; (j < nral); j++)
{
fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
}
}
else
{
for (j = 0; (j < 2); j++)
{
fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
}
}
fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
if (bt->param[i].s[0])
{
fprintf(out, " %s", bt->param[i].s);
}
else
{
for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET)); j++)
{
fprintf (out, "%13.6e ", bt->param[i].c[j]);
}
}
fprintf (out, "\n");
}
fprintf (out, "\n");
fflush (out);
}
void convert_harmonics(int nrmols, t_molinfo mols[], gpp_atomtype_t atype)
{
int n2m;
t_2morse *t2m;
int i, j, k, last, ni, nj;
int nrharm, nrmorse, bb;
real edis, kb, b0, beta;
gmx_bool *bRemoveHarm;
/* First get the data */
t2m = read_dissociation_energies(&n2m);
if (debug)
{
fprintf(debug, "MORSE: read %d dissoc energies\n", n2m);
}
if (n2m <= 0)
{
fprintf(stderr, "No dissocation energies read\n");
return;
}
/* For all the molecule types */
for (i = 0; (i < nrmols); i++)
{
/* Check how many morse and harmonic BONDSs there are, increase size of
* morse with the number of harmonics
*/
nrmorse = mols[i].plist[F_MORSE].nr;
for (bb = 0; (bb < F_NRE); bb++)
{
if ((interaction_function[bb].flags & IF_BTYPE) && (bb != F_MORSE))
{
nrharm = mols[i].plist[bb].nr;
pr_alloc(nrharm, &(mols[i].plist[F_MORSE]));
snew(bRemoveHarm, nrharm);
/* Now loop over the harmonics, trying to convert them */
for (j = 0; (j < nrharm); j++)
{
ni = mols[i].plist[bb].param[j].AI;
nj = mols[i].plist[bb].param[j].AJ;
edis =
search_e_diss(n2m, t2m,
get_atomtype_name(mols[i].atoms.atom[ni].type, atype),
get_atomtype_name(mols[i].atoms.atom[nj].type, atype));
if (edis != 0)
{
bRemoveHarm[j] = TRUE;
b0 = mols[i].plist[bb].param[j].c[0];
kb = mols[i].plist[bb].param[j].c[1];
beta = sqrt(kb/(2*edis));
mols[i].plist[F_MORSE].param[nrmorse].a[0] = ni;
mols[i].plist[F_MORSE].param[nrmorse].a[1] = nj;
mols[i].plist[F_MORSE].param[nrmorse].c[0] = b0;
mols[i].plist[F_MORSE].param[nrmorse].c[1] = edis;
mols[i].plist[F_MORSE].param[nrmorse].c[2] = beta;
nrmorse++;
}
}
mols[i].plist[F_MORSE].nr = nrmorse;
/* Now remove the harmonics */
for (j = last = 0; (j < nrharm); j++)
{
if (!bRemoveHarm[j])
{
/* Copy it to the last position */
for (k = 0; (k < MAXATOMLIST); k++)
{
mols[i].plist[bb].param[last].a[k] =
mols[i].plist[bb].param[j].a[k];
}
for (k = 0; (k < MAXFORCEPARAM); k++)
{
mols[i].plist[bb].param[last].c[k] =
mols[i].plist[bb].param[j].c[k];
}
last++;
}
}
sfree(bRemoveHarm);
fprintf(stderr, "Converted %d out of %d %s to morse bonds for mol %d\n",
nrharm-last, nrharm, interaction_function[bb].name, i);
mols[i].plist[bb].nr = last;
}
}
}
sfree(t2m);
}
static gmx_bool calc_vsite3out_param(gpp_atomtype_t atype,
t_param *param, t_atoms *at,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles)
{
/* i = virtual site | ,k
* j = 1st bonded heavy atom | i-j
* k,l = 2nd bonded atoms | `l
* NOTE: i is out of the j-k-l plane!
*/
gmx_bool bXH3,bError,bSwapParity;
real bij,bjk,bjl,aijk,aijl,akjl,pijk,pijl,a,b,c;
/* check if this is part of a NH2-umbrella, NH3 or CH3 group,
* i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
if (debug) {
int i;
for (i=0; i<4; i++)
fprintf(debug,"atom %u type %s ",
param->a[i]+1,get_atomtype_name(at->atom[param->a[i]].type,atype));
fprintf(debug,"\n");
}
bXH3 =
( (gmx_strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MNH",3)==0) &&
(gmx_strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MNH",3)==0) ) ||
( (gmx_strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MCH3",4)==0) &&
(gmx_strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MCH3",4)==0) );
/* check if construction parity must be swapped */
bSwapParity = ( param->C1 == -1 );
bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
bError = (bjk==NOTSET) || (bjl==NOTSET);
if (bXH3) {
/* now we get some XH3 group specific construction */
/* note: we call the heavy atom 'C' and the X atom 'N' */
real bMM,bCM,bCN,bNH,aCNH,dH,rH,rHx,rHy,dM,rM;
int aN;
/* check if bonds from heavy atom (j) to dummy masses (k,l) are equal: */
bError = bError || (bjk!=bjl);
/* the X atom (C or N) in the XH3 group is the first after the masses: */
aN = max(param->AK,param->AL)+1;
/* get all bondlengths and angles: */
bMM = get_bond_length(nrbond, bonds, param->AK, param->AL);
bCM = bjk;
bCN = get_bond_length(nrbond, bonds, param->AJ, aN);
bNH = get_bond_length(nrbond, bonds, aN, param->AI);
aCNH= get_angle (nrang, angles, param->AJ, aN, param->AI);
bError = bError ||
(bMM==NOTSET) || (bCN==NOTSET) || (bNH==NOTSET) || (aCNH==NOTSET);
/* calculate */
dH = bCN - bNH * cos(aCNH);
rH = bNH * sin(aCNH);
/* we assume the H's are symmetrically distributed */
rHx = rH*cos(DEG2RAD*30);
rHy = rH*sin(DEG2RAD*30);
rM = 0.5*bMM;
dM = sqrt( sqr(bCM) - sqr(rM) );
a = 0.5*( (dH/dM) - (rHy/rM) );
b = 0.5*( (dH/dM) + (rHy/rM) );
c = rHx / (2*dM*rM);
} else {
/* this is the general construction */
bij = get_bond_length(nrbond, bonds, param->AI, param->AJ);
aijk= get_angle (nrang, angles, param->AI, param->AJ, param->AK);
aijl= get_angle (nrang, angles, param->AI, param->AJ, param->AL);
akjl= get_angle (nrang, angles, param->AK, param->AJ, param->AL);
bError = bError ||
(bij==NOTSET) || (aijk==NOTSET) || (aijl==NOTSET) || (akjl==NOTSET);
pijk = cos(aijk)*bij;
pijl = cos(aijl)*bij;
a = ( pijk + (pijk*cos(akjl)-pijl) * cos(akjl) / sqr(sin(akjl)) ) / bjk;
b = ( pijl + (pijl*cos(akjl)-pijk) * cos(akjl) / sqr(sin(akjl)) ) / bjl;
c = - sqrt( sqr(bij) -
( sqr(pijk) - 2*pijk*pijl*cos(akjl) + sqr(pijl) )
/ sqr(sin(akjl)) )
/ ( bjk*bjl*sin(akjl) );
}
param->C0 = a;
param->C1 = b;
if (bSwapParity)
param->C2 = -c;
else
param->C2 = c;
if (debug)
fprintf(debug,"params for vsite3out %u: %g %g %g\n",
param->AI+1,param->C0,param->C1,param->C2);
return bError;
}
static gmx_bool calc_vsite3_param(gpp_atomtype_t atype,
t_param *param, t_atoms *at,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles )
{
/* i = virtual site | ,k
* j = 1st bonded heavy atom | i-j
* k,l = 2nd bonded atoms | `l
*/
gmx_bool bXH3,bError;
real bjk,bjl,a=-1,b=-1;
/* check if this is part of a NH3 , NH2-umbrella or CH3 group,
* i.e. if atom k and l are dummy masses (MNH* or MCH3*) */
if (debug) {
int i;
for (i=0; i<4; i++)
fprintf(debug,"atom %u type %s ",
param->a[i]+1,
get_atomtype_name(at->atom[param->a[i]].type,atype));
fprintf(debug,"\n");
}
bXH3 =
( (gmx_strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MNH",3)==0) &&
(gmx_strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MNH",3)==0) ) ||
( (gmx_strncasecmp(get_atomtype_name(at->atom[param->AK].type,atype),"MCH3",4)==0) &&
(gmx_strncasecmp(get_atomtype_name(at->atom[param->AL].type,atype),"MCH3",4)==0) );
bjk = get_bond_length(nrbond, bonds, param->AJ, param->AK);
bjl = get_bond_length(nrbond, bonds, param->AJ, param->AL);
bError = (bjk==NOTSET) || (bjl==NOTSET);
if (bXH3) {
/* now we get some XH2/XH3 group specific construction */
/* note: we call the heavy atom 'C' and the X atom 'N' */
real bMM,bCM,bCN,bNH,aCNH,dH,rH,dM,rM;
int aN;
/* check if bonds from heavy atom (j) to dummy masses (k,l) are equal: */
bError = bError || (bjk!=bjl);
/* the X atom (C or N) in the XH2/XH3 group is the first after the masses: */
aN = max(param->AK,param->AL)+1;
/* get common bonds */
bMM = get_bond_length(nrbond, bonds, param->AK, param->AL);
bCM = bjk;
bCN = get_bond_length(nrbond, bonds, param->AJ, aN);
bError = bError || (bMM==NOTSET) || (bCN==NOTSET);
/* calculate common things */
rM = 0.5*bMM;
dM = sqrt( sqr(bCM) - sqr(rM) );
/* are we dealing with the X atom? */
if ( param->AI == aN ) {
/* this is trivial */
a = b = 0.5 * bCN/dM;
} else {
/* get other bondlengths and angles: */
bNH = get_bond_length(nrbond, bonds, aN, param->AI);
aCNH= get_angle (nrang, angles, param->AJ, aN, param->AI);
bError = bError || (bNH==NOTSET) || (aCNH==NOTSET);
/* calculate */
dH = bCN - bNH * cos(aCNH);
rH = bNH * sin(aCNH);
a = 0.5 * ( dH/dM + rH/rM );
b = 0.5 * ( dH/dM - rH/rM );
}
} else
gmx_fatal(FARGS,"calc_vsite3_param not implemented for the general case "
"(atom %d)",param->AI+1);
param->C0 = a;
param->C1 = b;
if (debug)
fprintf(debug,"params for vsite3 %u: %g %g\n",
param->AI+1,param->C0,param->C1);
return bError;
}
