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45 #include "gromacs/utility/cstringutil.h"
46 #include "gen_vsite.h"
47 #include "gromacs/utility/smalloc.h"
55 #include "gromacs/utility/futil.h"
56 #include "gpp_atomtype.h"
57 #include "fflibutil.h"
60 #include "gromacs/utility/fatalerror.h"
63 #define OPENDIR '[' /* starting sign for directive */
64 #define CLOSEDIR ']' /* ending sign for directive */
67 char atomtype[MAXNAME]; /* Type for the XH3/XH2 atom */
68 gmx_bool isplanar; /* If true, the atomtype above and the three connected
69 * ones are in a planar geometry. The two next entries
70 * are undefined in that case
72 int nhydrogens; /* number of connected hydrogens */
73 char nextheavytype[MAXNAME]; /* Type for the heavy atom bonded to XH2/XH3 */
74 char dummymass[MAXNAME]; /* The type of MNH* or MCH3* dummy mass to use */
78 /* Structure to represent average bond and angles values in vsite aromatic
79 * residues. Note that these are NOT necessarily the bonds and angles from the
80 * forcefield; many forcefields (like Amber, OPLS) have some inherent strain in
81 * 5-rings (i.e. the sum of angles is !=540, but impropers keep it planar)
84 char resname[MAXNAME];
87 struct vsitetop_bond {
91 } *bond; /* list of bonds */
92 struct vsitetop_angle {
97 } *angle; /* list of angles */
102 DDB_CH3, DDB_NH3, DDB_NH2, DDB_PHE, DDB_TYR,
103 DDB_TRP, DDB_HISA, DDB_HISB, DDB_HISH, DDB_DIR_NR
106 typedef char t_dirname[STRLEN];
108 static const t_dirname ddb_dirnames[DDB_DIR_NR] = {
120 static int ddb_name2dir(char *name)
122 /* Translate a directive name to the number of the directive.
123 * HID/HIE/HIP names are translated to the ones we use in Gromacs.
130 for (i = 0; i < DDB_DIR_NR && index < 0; i++)
132 if (!gmx_strcasecmp(name, ddb_dirnames[i]))
142 static void read_vsite_database(const char *ddbname,
143 t_vsiteconf **pvsiteconflist, int *nvsiteconf,
144 t_vsitetop **pvsitetoplist, int *nvsitetop)
146 /* This routine is a quick hack to fix the problem with hardcoded atomtypes
147 * and aromatic vsite parameters by reading them from a ff???.vsd file.
149 * The file can contain sections [ NH3 ], [ CH3 ], [ NH2 ], and ring residue names.
150 * For the NH3 and CH3 section each line has three fields. The first is the atomtype
151 * (nb: not bonded type) of the N/C atom to be replaced, the second field is
152 * the type of the next heavy atom it is bonded to, and the third field the type
153 * of dummy mass that will be used for this group.
155 * If the NH2 group planar (sp2 N) a different vsite construct is used, so in this
156 * case the second field should just be the word planar.
162 int i, j, n, k, nvsite, ntop, curdir, prevdir;
163 t_vsiteconf *vsiteconflist;
164 t_vsitetop *vsitetoplist;
166 char s1[MAXNAME], s2[MAXNAME], s3[MAXNAME], s4[MAXNAME];
168 ddb = libopen(ddbname);
170 nvsite = *nvsiteconf;
171 vsiteconflist = *pvsiteconflist;
173 vsitetoplist = *pvsitetoplist;
177 snew(vsiteconflist, 1);
178 snew(vsitetoplist, 1);
180 while (fgets2(pline, STRLEN-2, ddb) != NULL)
182 strip_comment(pline);
184 if (strlen(pline) > 0)
186 if (pline[0] == OPENDIR)
188 strncpy(dirstr, pline+1, STRLEN-2);
189 if ((ch = strchr (dirstr, CLOSEDIR)) != NULL)
195 if (!gmx_strcasecmp(dirstr, "HID") ||
196 !gmx_strcasecmp(dirstr, "HISD"))
198 sprintf(dirstr, "HISA");
200 else if (!gmx_strcasecmp(dirstr, "HIE") ||
201 !gmx_strcasecmp(dirstr, "HISE"))
203 sprintf(dirstr, "HISB");
205 else if (!gmx_strcasecmp(dirstr, "HIP"))
207 sprintf(dirstr, "HISH");
210 curdir = ddb_name2dir(dirstr);
213 gmx_fatal(FARGS, "Invalid directive %s in vsite database %s",
222 gmx_fatal(FARGS, "First entry in vsite database must be a directive.\n");
227 n = sscanf(pline, "%s%s%s", s1, s2, s3);
228 if (n < 3 && !gmx_strcasecmp(s2, "planar"))
230 srenew(vsiteconflist, nvsite+1);
231 strncpy(vsiteconflist[nvsite].atomtype, s1, MAXNAME-1);
232 vsiteconflist[nvsite].isplanar = TRUE;
233 vsiteconflist[nvsite].nextheavytype[0] = 0;
234 vsiteconflist[nvsite].dummymass[0] = 0;
235 vsiteconflist[nvsite].nhydrogens = 2;
240 srenew(vsiteconflist, (nvsite+1));
241 strncpy(vsiteconflist[nvsite].atomtype, s1, MAXNAME-1);
242 vsiteconflist[nvsite].isplanar = FALSE;
243 strncpy(vsiteconflist[nvsite].nextheavytype, s2, MAXNAME-1);
244 strncpy(vsiteconflist[nvsite].dummymass, s3, MAXNAME-1);
245 if (curdir == DDB_NH2)
247 vsiteconflist[nvsite].nhydrogens = 2;
251 vsiteconflist[nvsite].nhydrogens = 3;
257 gmx_fatal(FARGS, "Not enough directives in vsite database line: %s\n", pline);
267 while ((i < ntop) && gmx_strcasecmp(dirstr, vsitetoplist[i].resname))
271 /* Allocate a new topology entry if this is a new residue */
274 srenew(vsitetoplist, ntop+1);
275 ntop++; /* i still points to current vsite topology entry */
276 strncpy(vsitetoplist[i].resname, dirstr, MAXNAME-1);
277 vsitetoplist[i].nbonds = vsitetoplist[i].nangles = 0;
278 snew(vsitetoplist[i].bond, 1);
279 snew(vsitetoplist[i].angle, 1);
281 n = sscanf(pline, "%s%s%s%s", s1, s2, s3, s4);
285 k = vsitetoplist[i].nbonds++;
286 srenew(vsitetoplist[i].bond, k+1);
287 strncpy(vsitetoplist[i].bond[k].atom1, s1, MAXNAME-1);
288 strncpy(vsitetoplist[i].bond[k].atom2, s2, MAXNAME-1);
289 vsitetoplist[i].bond[k].value = strtod(s3, NULL);
294 k = vsitetoplist[i].nangles++;
295 srenew(vsitetoplist[i].angle, k+1);
296 strncpy(vsitetoplist[i].angle[k].atom1, s1, MAXNAME-1);
297 strncpy(vsitetoplist[i].angle[k].atom2, s2, MAXNAME-1);
298 strncpy(vsitetoplist[i].angle[k].atom3, s3, MAXNAME-1);
299 vsitetoplist[i].angle[k].value = strtod(s4, NULL);
303 gmx_fatal(FARGS, "Need 3 or 4 values to specify bond/angle values in %s: %s\n", ddbname, pline);
307 gmx_fatal(FARGS, "Didnt find a case for directive %s in read_vsite_database\n", dirstr);
313 *pvsiteconflist = vsiteconflist;
314 *pvsitetoplist = vsitetoplist;
315 *nvsiteconf = nvsite;
321 static int nitrogen_is_planar(t_vsiteconf vsiteconflist[], int nvsiteconf, char atomtype[])
323 /* Return 1 if atomtype exists in database list and is planar, 0 if not,
324 * and -1 if not found.
327 gmx_bool found = FALSE;
328 for (i = 0; i < nvsiteconf && !found; i++)
330 found = (!gmx_strcasecmp(vsiteconflist[i].atomtype, atomtype) && (vsiteconflist[i].nhydrogens == 2));
334 res = (vsiteconflist[i-1].isplanar == TRUE);
344 static char *get_dummymass_name(t_vsiteconf vsiteconflist[], int nvsiteconf, char atom[], char nextheavy[])
346 /* Return the dummy mass name if found, or NULL if not set in ddb database */
348 gmx_bool found = FALSE;
349 for (i = 0; i < nvsiteconf && !found; i++)
351 found = (!gmx_strcasecmp(vsiteconflist[i].atomtype, atom) &&
352 !gmx_strcasecmp(vsiteconflist[i].nextheavytype, nextheavy));
356 return vsiteconflist[i-1].dummymass;
366 static real get_ddb_bond(t_vsitetop *vsitetop, int nvsitetop,
368 const char atom1[], const char atom2[])
373 while (i < nvsitetop && gmx_strcasecmp(res, vsitetop[i].resname))
379 gmx_fatal(FARGS, "No vsite information for residue %s found in vsite database.\n", res);
382 while (j < vsitetop[i].nbonds &&
383 ( strcmp(atom1, vsitetop[i].bond[j].atom1) || strcmp(atom2, vsitetop[i].bond[j].atom2)) &&
384 ( strcmp(atom2, vsitetop[i].bond[j].atom1) || strcmp(atom1, vsitetop[i].bond[j].atom2)))
388 if (j == vsitetop[i].nbonds)
390 gmx_fatal(FARGS, "Couldnt find bond %s-%s for residue %s in vsite database.\n", atom1, atom2, res);
393 return vsitetop[i].bond[j].value;
397 static real get_ddb_angle(t_vsitetop *vsitetop, int nvsitetop,
398 const char res[], const char atom1[],
399 const char atom2[], const char atom3[])
404 while (i < nvsitetop && gmx_strcasecmp(res, vsitetop[i].resname))
410 gmx_fatal(FARGS, "No vsite information for residue %s found in vsite database.\n", res);
413 while (j < vsitetop[i].nangles &&
414 ( strcmp(atom1, vsitetop[i].angle[j].atom1) ||
415 strcmp(atom2, vsitetop[i].angle[j].atom2) ||
416 strcmp(atom3, vsitetop[i].angle[j].atom3)) &&
417 ( strcmp(atom3, vsitetop[i].angle[j].atom1) ||
418 strcmp(atom2, vsitetop[i].angle[j].atom2) ||
419 strcmp(atom1, vsitetop[i].angle[j].atom3)))
423 if (j == vsitetop[i].nangles)
425 gmx_fatal(FARGS, "Couldnt find angle %s-%s-%s for residue %s in vsite database.\n", atom1, atom2, atom3, res);
428 return vsitetop[i].angle[j].value;
432 static void count_bonds(int atom, t_params *psb, char ***atomname,
433 int *nrbonds, int *nrHatoms, int Hatoms[], int *Heavy,
434 int *nrheavies, int heavies[])
436 int i, heavy, other, nrb, nrH, nrhv;
438 /* find heavy atom bound to this hydrogen */
440 for (i = 0; (i < psb->nr) && (heavy == NOTSET); i++)
442 if (psb->param[i].AI == atom)
444 heavy = psb->param[i].AJ;
446 else if (psb->param[i].AJ == atom)
448 heavy = psb->param[i].AI;
453 gmx_fatal(FARGS, "unbound hydrogen atom %d", atom+1);
455 /* find all atoms bound to heavy atom */
460 for (i = 0; i < psb->nr; i++)
462 if (psb->param[i].AI == heavy)
464 other = psb->param[i].AJ;
466 else if (psb->param[i].AJ == heavy)
468 other = psb->param[i].AI;
473 if (is_hydrogen(*(atomname[other])))
480 heavies[nrhv] = other;
492 static void print_bonds(FILE *fp, int o2n[],
493 int nrHatoms, int Hatoms[], int Heavy,
494 int nrheavies, int heavies[])
498 fprintf(fp, "Found: %d Hatoms: ", nrHatoms);
499 for (i = 0; i < nrHatoms; i++)
501 fprintf(fp, " %d", o2n[Hatoms[i]]+1);
503 fprintf(fp, "; %d Heavy atoms: %d", nrheavies+1, o2n[Heavy]+1);
504 for (i = 0; i < nrheavies; i++)
506 fprintf(fp, " %d", o2n[heavies[i]]+1);
511 static int get_atype(int atom, t_atoms *at, int nrtp, t_restp rtp[],
512 gmx_residuetype_t rt)
519 if (at->atom[atom].m)
521 type = at->atom[atom].type;
525 /* get type from rtp */
526 rtpp = get_restp(*(at->resinfo[at->atom[atom].resind].name), nrtp, rtp);
527 bNterm = gmx_residuetype_is_protein(rt, *(at->resinfo[at->atom[atom].resind].name)) &&
528 (at->atom[atom].resind == 0);
529 j = search_jtype(rtpp, *(at->atomname[atom]), bNterm);
530 type = rtpp->atom[j].type;
535 static int vsite_nm2type(const char *name, gpp_atomtype_t atype)
539 tp = get_atomtype_type(name, atype);
542 gmx_fatal(FARGS, "Dummy mass type (%s) not found in atom type database",
549 static real get_amass(int atom, t_atoms *at, int nrtp, t_restp rtp[],
550 gmx_residuetype_t rt)
557 if (at->atom[atom].m)
559 mass = at->atom[atom].m;
563 /* get mass from rtp */
564 rtpp = get_restp(*(at->resinfo[at->atom[atom].resind].name), nrtp, rtp);
565 bNterm = gmx_residuetype_is_protein(rt, *(at->resinfo[at->atom[atom].resind].name)) &&
566 (at->atom[atom].resind == 0);
567 j = search_jtype(rtpp, *(at->atomname[atom]), bNterm);
568 mass = rtpp->atom[j].m;
573 static void my_add_param(t_params *plist, int ai, int aj, real b)
575 static real c[MAXFORCEPARAM] =
576 { NOTSET, NOTSET, NOTSET, NOTSET, NOTSET, NOTSET };
579 add_param(plist, ai, aj, c, NULL);
582 static void add_vsites(t_params plist[], int vsite_type[],
583 int Heavy, int nrHatoms, int Hatoms[],
584 int nrheavies, int heavies[])
586 int i, j, ftype, other, moreheavy, bb;
587 gmx_bool bSwapParity;
589 for (i = 0; i < nrHatoms; i++)
591 ftype = vsite_type[Hatoms[i]];
592 /* Errors in setting the vsite_type should really be caugth earlier,
593 * because here it's not possible to print any useful error message.
594 * But it's still better to print a message than to segfault.
598 gmx_incons("Undetected error in setting up virtual sites");
600 bSwapParity = (ftype < 0);
601 vsite_type[Hatoms[i]] = ftype = abs(ftype);
602 if (ftype == F_BONDS)
604 if ( (nrheavies != 1) && (nrHatoms != 1) )
606 gmx_fatal(FARGS, "cannot make constraint in add_vsites for %d heavy "
607 "atoms and %d hydrogen atoms", nrheavies, nrHatoms);
609 my_add_param(&(plist[F_CONSTRNC]), Hatoms[i], heavies[0], NOTSET);
620 gmx_fatal(FARGS, "Not enough heavy atoms (%d) for %s (min 3)",
622 interaction_function[vsite_type[Hatoms[i]]].name);
624 add_vsite3_atoms(&plist[ftype], Hatoms[i], Heavy, heavies[0], heavies[1],
631 moreheavy = heavies[1];
635 /* find more heavy atoms */
636 other = moreheavy = NOTSET;
637 for (j = 0; (j < plist[F_BONDS].nr) && (moreheavy == NOTSET); j++)
639 if (plist[F_BONDS].param[j].AI == heavies[0])
641 other = plist[F_BONDS].param[j].AJ;
643 else if (plist[F_BONDS].param[j].AJ == heavies[0])
645 other = plist[F_BONDS].param[j].AI;
647 if ( (other != NOTSET) && (other != Heavy) )
652 if (moreheavy == NOTSET)
654 gmx_fatal(FARGS, "Unbound molecule part %d-%d", Heavy+1, Hatoms[0]+1);
657 add_vsite3_atoms(&plist[ftype], Hatoms[i], Heavy, heavies[0], moreheavy,
665 gmx_fatal(FARGS, "Not enough heavy atoms (%d) for %s (min 4)",
667 interaction_function[vsite_type[Hatoms[i]]].name);
669 add_vsite4_atoms(&plist[ftype],
670 Hatoms[0], Heavy, heavies[0], heavies[1], heavies[2]);
674 gmx_fatal(FARGS, "can't use add_vsites for interaction function %s",
675 interaction_function[vsite_type[Hatoms[i]]].name);
681 #define ANGLE_6RING (DEG2RAD*120)
683 /* cosine rule: a^2 = b^2 + c^2 - 2 b c cos(alpha) */
684 /* get a^2 when a, b and alpha are given: */
685 #define cosrule(b, c, alpha) ( sqr(b) + sqr(c) - 2*b*c*cos(alpha) )
686 /* get cos(alpha) when a, b and c are given: */
687 #define acosrule(a, b, c) ( (sqr(b)+sqr(c)-sqr(a))/(2*b*c) )
689 static int gen_vsites_6ring(t_atoms *at, int *vsite_type[], t_params plist[],
690 int nrfound, int *ats, real bond_cc, real bond_ch,
691 real xcom, gmx_bool bDoZ)
693 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
695 atCG, atCD1, atHD1, atCD2, atHD2, atCE1, atHE1, atCE2, atHE2,
700 real a, b, dCGCE, tmp1, tmp2, mtot, mG, mrest;
701 real xCG, yCG, xCE1, yCE1, xCE2, yCE2;
702 /* CG, CE1 and CE2 stay and each get a part of the total mass,
703 * so the c-o-m stays the same.
710 gmx_incons("Generating vsites on 6-rings");
714 /* constraints between CG, CE1 and CE2: */
715 dCGCE = sqrt( cosrule(bond_cc, bond_cc, ANGLE_6RING) );
716 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atCE1], dCGCE);
717 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atCE2], dCGCE);
718 my_add_param(&(plist[F_CONSTRNC]), ats[atCE1], ats[atCE2], dCGCE);
720 /* rest will be vsite3 */
723 for (i = 0; i < (bDoZ ? atNR : atHZ); i++)
725 mtot += at->atom[ats[i]].m;
726 if (i != atCG && i != atCE1 && i != atCE2 && (bDoZ || (i != atHZ && i != atCZ) ) )
728 at->atom[ats[i]].m = at->atom[ats[i]].mB = 0;
729 (*vsite_type)[ats[i]] = F_VSITE3;
733 /* Distribute mass so center-of-mass stays the same.
734 * The center-of-mass in the call is defined with x=0 at
735 * the CE1-CE2 bond and y=0 at the line from CG to the middle of CE1-CE2 bond.
737 xCG = -bond_cc+bond_cc*cos(ANGLE_6RING);
740 yCE1 = bond_cc*sin(0.5*ANGLE_6RING);
742 yCE2 = -bond_cc*sin(0.5*ANGLE_6RING);
744 mG = at->atom[ats[atCG]].m = at->atom[ats[atCG]].mB = xcom*mtot/xCG;
746 at->atom[ats[atCE1]].m = at->atom[ats[atCE1]].mB =
747 at->atom[ats[atCE2]].m = at->atom[ats[atCE2]].mB = mrest / 2;
749 /* vsite3 construction: r_d = r_i + a r_ij + b r_ik */
750 tmp1 = dCGCE*sin(ANGLE_6RING*0.5);
751 tmp2 = bond_cc*cos(0.5*ANGLE_6RING) + tmp1;
753 a = b = -bond_ch / tmp1;
755 add_vsite3_param(&plist[F_VSITE3],
756 ats[atHE1], ats[atCE1], ats[atCE2], ats[atCG], a, b);
757 add_vsite3_param(&plist[F_VSITE3],
758 ats[atHE2], ats[atCE2], ats[atCE1], ats[atCG], a, b);
759 /* CD1, CD2 and CZ: */
761 add_vsite3_param(&plist[F_VSITE3],
762 ats[atCD1], ats[atCE2], ats[atCE1], ats[atCG], a, b);
763 add_vsite3_param(&plist[F_VSITE3],
764 ats[atCD2], ats[atCE1], ats[atCE2], ats[atCG], a, b);
767 add_vsite3_param(&plist[F_VSITE3],
768 ats[atCZ], ats[atCG], ats[atCE1], ats[atCE2], a, b);
770 /* HD1, HD2 and HZ: */
771 a = b = ( bond_ch + tmp2 ) / tmp1;
772 add_vsite3_param(&plist[F_VSITE3],
773 ats[atHD1], ats[atCE2], ats[atCE1], ats[atCG], a, b);
774 add_vsite3_param(&plist[F_VSITE3],
775 ats[atHD2], ats[atCE1], ats[atCE2], ats[atCG], a, b);
778 add_vsite3_param(&plist[F_VSITE3],
779 ats[atHZ], ats[atCG], ats[atCE1], ats[atCE2], a, b);
785 static int gen_vsites_phe(t_atoms *at, int *vsite_type[], t_params plist[],
786 int nrfound, int *ats, t_vsitetop *vsitetop, int nvsitetop)
788 real bond_cc, bond_ch;
791 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
793 atCG, atCD1, atHD1, atCD2, atHD2, atCE1, atHE1, atCE2, atHE2,
796 real x[atNR], y[atNR];
797 /* Aromatic rings have 6-fold symmetry, so we only need one bond length.
798 * (angle is always 120 degrees).
800 bond_cc = get_ddb_bond(vsitetop, nvsitetop, "PHE", "CD1", "CE1");
801 bond_ch = get_ddb_bond(vsitetop, nvsitetop, "PHE", "CD1", "HD1");
803 x[atCG] = -bond_cc+bond_cc*cos(ANGLE_6RING);
806 y[atCD1] = bond_cc*sin(0.5*ANGLE_6RING);
807 x[atHD1] = x[atCD1]+bond_ch*cos(ANGLE_6RING);
808 y[atHD1] = y[atCD1]+bond_ch*sin(ANGLE_6RING);
811 x[atHE1] = x[atCE1]-bond_ch*cos(ANGLE_6RING);
812 y[atHE1] = y[atCE1]+bond_ch*sin(ANGLE_6RING);
814 y[atCD2] = -y[atCD1];
816 y[atHD2] = -y[atHD1];
818 y[atCE2] = -y[atCE1];
820 y[atHE2] = -y[atHE1];
821 x[atCZ] = bond_cc*cos(0.5*ANGLE_6RING);
823 x[atHZ] = x[atCZ]+bond_ch;
827 for (i = 0; i < atNR; i++)
829 xcom += x[i]*at->atom[ats[i]].m;
830 mtot += at->atom[ats[i]].m;
834 return gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, TRUE);
837 static void calc_vsite3_param(real xd, real yd, real xi, real yi, real xj, real yj,
838 real xk, real yk, real *a, real *b)
840 /* determine parameters by solving the equation system, since we know the
841 * virtual site coordinates here.
843 real dx_ij, dx_ik, dy_ij, dy_ik;
850 b_ij = sqrt(dx_ij*dx_ij+dy_ij*dy_ij);
851 b_ik = sqrt(dx_ik*dx_ik+dy_ik*dy_ik);
853 *a = ( (xd-xi)*dy_ik - dx_ik*(yd-yi) ) / (dx_ij*dy_ik - dx_ik*dy_ij);
854 *b = ( yd - yi - (*a)*dy_ij ) / dy_ik;
858 static int gen_vsites_trp(gpp_atomtype_t atype, rvec *newx[],
859 t_atom *newatom[], char ***newatomname[],
860 int *o2n[], int *newvsite_type[], int *newcgnr[],
861 t_symtab *symtab, int *nadd, rvec x[], int *cgnr[],
862 t_atoms *at, int *vsite_type[], t_params plist[],
863 int nrfound, int *ats, int add_shift,
864 t_vsitetop *vsitetop, int nvsitetop)
867 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
869 atCB, atCG, atCD1, atHD1, atCD2, atNE1, atHE1, atCE2, atCE3, atHE3,
870 atCZ2, atHZ2, atCZ3, atHZ3, atCH2, atHH2, atNR
872 /* weights for determining the COM's of both rings (M1 and M2): */
873 real mw[NMASS][atNR] = {
874 { 0, 1, 1, 1, 0.5, 1, 1, 0.5, 0, 0,
876 { 0, 0, 0, 0, 0.5, 0, 0, 0.5, 1, 1,
880 real xi[atNR], yi[atNR];
881 real xcom[NMASS], ycom[NMASS], I, alpha;
882 real lineA, lineB, dist;
883 real b_CD2_CE2, b_NE1_CE2, b_CG_CD2, b_CH2_HH2, b_CE2_CZ2;
884 real b_NE1_HE1, b_CD2_CE3, b_CE3_CZ3, b_CB_CG;
885 real b_CZ2_CH2, b_CZ2_HZ2, b_CD1_HD1, b_CE3_HE3;
886 real b_CG_CD1, b_CZ3_HZ3;
887 real a_NE1_CE2_CD2, a_CE2_CD2_CG, a_CB_CG_CD2, a_CE2_CD2_CE3;
888 real a_CB_CG_CD1, a_CD2_CG_CD1, a_CE2_CZ2_HZ2, a_CZ2_CH2_HH2;
889 real a_CD2_CE2_CZ2, a_CD2_CE3_CZ3, a_CE3_CZ3_HZ3, a_CG_CD1_HD1;
890 real a_CE2_CZ2_CH2, a_HE1_NE1_CE2, a_CD2_CE3_HE3;
892 int atM[NMASS], tpM, i, i0, j, nvsite;
893 real mwtot, mtot, mM[NMASS], dCBM1, dCBM2, dM1M2;
894 real a, b, c[MAXFORCEPARAM];
895 rvec r_ij, r_ik, t1, t2;
900 gmx_incons("atom types in gen_vsites_trp");
902 /* Get geometry from database */
903 b_CD2_CE2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CD2", "CE2");
904 b_NE1_CE2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "NE1", "CE2");
905 b_CG_CD1 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CG", "CD1");
906 b_CG_CD2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CG", "CD2");
907 b_CB_CG = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CB", "CG");
908 b_CE2_CZ2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CE2", "CZ2");
909 b_CD2_CE3 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CD2", "CE3");
910 b_CE3_CZ3 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CE3", "CZ3");
911 b_CZ2_CH2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CZ2", "CH2");
913 b_CD1_HD1 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CD1", "HD1");
914 b_CZ2_HZ2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CZ2", "HZ2");
915 b_NE1_HE1 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "NE1", "HE1");
916 b_CH2_HH2 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CH2", "HH2");
917 b_CE3_HE3 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CE3", "HE3");
918 b_CZ3_HZ3 = get_ddb_bond(vsitetop, nvsitetop, "TRP", "CZ3", "HZ3");
920 a_NE1_CE2_CD2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "NE1", "CE2", "CD2");
921 a_CE2_CD2_CG = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CE2", "CD2", "CG");
922 a_CB_CG_CD2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CB", "CG", "CD2");
923 a_CD2_CG_CD1 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CD2", "CG", "CD1");
924 a_CB_CG_CD1 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CB", "CG", "CD1");
926 a_CE2_CD2_CE3 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CE2", "CD2", "CE3");
927 a_CD2_CE2_CZ2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CD2", "CE2", "CZ2");
928 a_CD2_CE3_CZ3 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CD2", "CE3", "CZ3");
929 a_CE3_CZ3_HZ3 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CE3", "CZ3", "HZ3");
930 a_CZ2_CH2_HH2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CZ2", "CH2", "HH2");
931 a_CE2_CZ2_HZ2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CE2", "CZ2", "HZ2");
932 a_CE2_CZ2_CH2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CE2", "CZ2", "CH2");
933 a_CG_CD1_HD1 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CG", "CD1", "HD1");
934 a_HE1_NE1_CE2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "HE1", "NE1", "CE2");
935 a_CD2_CE3_HE3 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TRP", "CD2", "CE3", "HE3");
937 /* Calculate local coordinates.
938 * y-axis (x=0) is the bond CD2-CE2.
939 * x-axis (y=0) is perpendicular to the bond CD2-CE2 and
940 * intersects the middle of the bond.
943 yi[atCD2] = -0.5*b_CD2_CE2;
946 yi[atCE2] = 0.5*b_CD2_CE2;
948 xi[atNE1] = -b_NE1_CE2*sin(a_NE1_CE2_CD2);
949 yi[atNE1] = yi[atCE2]-b_NE1_CE2*cos(a_NE1_CE2_CD2);
951 xi[atCG] = -b_CG_CD2*sin(a_CE2_CD2_CG);
952 yi[atCG] = yi[atCD2]+b_CG_CD2*cos(a_CE2_CD2_CG);
954 alpha = a_CE2_CD2_CG + M_PI - a_CB_CG_CD2;
955 xi[atCB] = xi[atCG]-b_CB_CG*sin(alpha);
956 yi[atCB] = yi[atCG]+b_CB_CG*cos(alpha);
958 alpha = a_CE2_CD2_CG + a_CD2_CG_CD1 - M_PI;
959 xi[atCD1] = xi[atCG]-b_CG_CD1*sin(alpha);
960 yi[atCD1] = yi[atCG]+b_CG_CD1*cos(alpha);
962 xi[atCE3] = b_CD2_CE3*sin(a_CE2_CD2_CE3);
963 yi[atCE3] = yi[atCD2]+b_CD2_CE3*cos(a_CE2_CD2_CE3);
965 xi[atCZ2] = b_CE2_CZ2*sin(a_CD2_CE2_CZ2);
966 yi[atCZ2] = yi[atCE2]-b_CE2_CZ2*cos(a_CD2_CE2_CZ2);
968 alpha = a_CE2_CD2_CE3 + a_CD2_CE3_CZ3 - M_PI;
969 xi[atCZ3] = xi[atCE3]+b_CE3_CZ3*sin(alpha);
970 yi[atCZ3] = yi[atCE3]+b_CE3_CZ3*cos(alpha);
972 alpha = a_CD2_CE2_CZ2 + a_CE2_CZ2_CH2 - M_PI;
973 xi[atCH2] = xi[atCZ2]+b_CZ2_CH2*sin(alpha);
974 yi[atCH2] = yi[atCZ2]-b_CZ2_CH2*cos(alpha);
977 alpha = a_CE2_CD2_CG + a_CD2_CG_CD1 - a_CG_CD1_HD1;
978 xi[atHD1] = xi[atCD1]-b_CD1_HD1*sin(alpha);
979 yi[atHD1] = yi[atCD1]+b_CD1_HD1*cos(alpha);
981 alpha = a_NE1_CE2_CD2 + M_PI - a_HE1_NE1_CE2;
982 xi[atHE1] = xi[atNE1]-b_NE1_HE1*sin(alpha);
983 yi[atHE1] = yi[atNE1]-b_NE1_HE1*cos(alpha);
985 alpha = a_CE2_CD2_CE3 + M_PI - a_CD2_CE3_HE3;
986 xi[atHE3] = xi[atCE3]+b_CE3_HE3*sin(alpha);
987 yi[atHE3] = yi[atCE3]+b_CE3_HE3*cos(alpha);
989 alpha = a_CD2_CE2_CZ2 + M_PI - a_CE2_CZ2_HZ2;
990 xi[atHZ2] = xi[atCZ2]+b_CZ2_HZ2*sin(alpha);
991 yi[atHZ2] = yi[atCZ2]-b_CZ2_HZ2*cos(alpha);
993 alpha = a_CD2_CE2_CZ2 + a_CE2_CZ2_CH2 - a_CZ2_CH2_HH2;
994 xi[atHZ3] = xi[atCZ3]+b_CZ3_HZ3*sin(alpha);
995 yi[atHZ3] = yi[atCZ3]+b_CZ3_HZ3*cos(alpha);
997 alpha = a_CE2_CD2_CE3 + a_CD2_CE3_CZ3 - a_CE3_CZ3_HZ3;
998 xi[atHH2] = xi[atCH2]+b_CH2_HH2*sin(alpha);
999 yi[atHH2] = yi[atCH2]-b_CH2_HH2*cos(alpha);
1001 /* Determine coeff. for the line CB-CG */
1002 lineA = (yi[atCB]-yi[atCG])/(xi[atCB]-xi[atCG]);
1003 lineB = yi[atCG]-lineA*xi[atCG];
1005 /* Calculate masses for each ring and put it on the dummy masses */
1006 for (j = 0; j < NMASS; j++)
1008 mM[j] = xcom[j] = ycom[j] = 0;
1010 for (i = 0; i < atNR; i++)
1014 for (j = 0; j < NMASS; j++)
1016 mM[j] += mw[j][i] * at->atom[ats[i]].m;
1017 xcom[j] += xi[i] * mw[j][i] * at->atom[ats[i]].m;
1018 ycom[j] += yi[i] * mw[j][i] * at->atom[ats[i]].m;
1022 for (j = 0; j < NMASS; j++)
1028 /* get dummy mass type */
1029 tpM = vsite_nm2type("MW", atype);
1030 /* make space for 2 masses: shift all atoms starting with CB */
1032 for (j = 0; j < NMASS; j++)
1034 atM[j] = i0+*nadd+j;
1038 fprintf(stderr, "Inserting %d dummy masses at %d\n", NMASS, (*o2n)[i0]+1);
1041 for (j = i0; j < at->nr; j++)
1043 (*o2n)[j] = j+*nadd;
1045 srenew(*newx, at->nr+*nadd);
1046 srenew(*newatom, at->nr+*nadd);
1047 srenew(*newatomname, at->nr+*nadd);
1048 srenew(*newvsite_type, at->nr+*nadd);
1049 srenew(*newcgnr, at->nr+*nadd);
1050 for (j = 0; j < NMASS; j++)
1052 (*newatomname)[at->nr+*nadd-1-j] = NULL;
1055 /* Dummy masses will be placed at the center-of-mass in each ring. */
1057 /* calc initial position for dummy masses in real (non-local) coordinates.
1058 * Cheat by using the routine to calculate virtual site parameters. It is
1059 * much easier when we have the coordinates expressed in terms of
1062 rvec_sub(x[ats[atCB]], x[ats[atCG]], r_ij);
1063 rvec_sub(x[ats[atCD2]], x[ats[atCG]], r_ik);
1064 calc_vsite3_param(xcom[0], ycom[0], xi[atCG], yi[atCG], xi[atCB], yi[atCB],
1065 xi[atCD2], yi[atCD2], &a, &b);
1068 rvec_add(t1, t2, t1);
1069 rvec_add(t1, x[ats[atCG]], (*newx)[atM[0]]);
1071 calc_vsite3_param(xcom[1], ycom[1], xi[atCG], yi[atCG], xi[atCB], yi[atCB],
1072 xi[atCD2], yi[atCD2], &a, &b);
1075 rvec_add(t1, t2, t1);
1076 rvec_add(t1, x[ats[atCG]], (*newx)[atM[1]]);
1078 /* set parameters for the masses */
1079 for (j = 0; j < NMASS; j++)
1081 sprintf(name, "MW%d", j+1);
1082 (*newatomname) [atM[j]] = put_symtab(symtab, name);
1083 (*newatom) [atM[j]].m = (*newatom)[atM[j]].mB = mM[j];
1084 (*newatom) [atM[j]].q = (*newatom)[atM[j]].qB = 0.0;
1085 (*newatom) [atM[j]].type = (*newatom)[atM[j]].typeB = tpM;
1086 (*newatom) [atM[j]].ptype = eptAtom;
1087 (*newatom) [atM[j]].resind = at->atom[i0].resind;
1088 (*newatom) [atM[j]].elem[0] = 'M';
1089 (*newatom) [atM[j]].elem[1] = '\0';
1090 (*newvsite_type)[atM[j]] = NOTSET;
1091 (*newcgnr) [atM[j]] = (*cgnr)[i0];
1093 /* renumber cgnr: */
1094 for (i = i0; i < at->nr; i++)
1099 /* constraints between CB, M1 and M2 */
1100 /* 'add_shift' says which atoms won't be renumbered afterwards */
1101 dCBM1 = sqrt( sqr(xcom[0]-xi[atCB]) + sqr(ycom[0]-yi[atCB]) );
1102 dM1M2 = sqrt( sqr(xcom[0]-xcom[1]) + sqr(ycom[0]-ycom[1]) );
1103 dCBM2 = sqrt( sqr(xcom[1]-xi[atCB]) + sqr(ycom[1]-yi[atCB]) );
1104 my_add_param(&(plist[F_CONSTRNC]), ats[atCB], add_shift+atM[0], dCBM1);
1105 my_add_param(&(plist[F_CONSTRNC]), ats[atCB], add_shift+atM[1], dCBM2);
1106 my_add_param(&(plist[F_CONSTRNC]), add_shift+atM[0], add_shift+atM[1], dM1M2);
1108 /* rest will be vsite3 */
1110 for (i = 0; i < atNR; i++)
1114 at->atom[ats[i]].m = at->atom[ats[i]].mB = 0;
1115 (*vsite_type)[ats[i]] = F_VSITE3;
1120 /* now define all vsites from M1, M2, CB, ie:
1121 r_d = r_M1 + a r_M1_M2 + b r_M1_CB */
1122 for (i = 0; i < atNR; i++)
1124 if ( (*vsite_type)[ats[i]] == F_VSITE3)
1126 calc_vsite3_param(xi[i], yi[i], xcom[0], ycom[0], xcom[1], ycom[1], xi[atCB], yi[atCB], &a, &b);
1127 add_vsite3_param(&plist[F_VSITE3],
1128 ats[i], add_shift+atM[0], add_shift+atM[1], ats[atCB], a, b);
1136 static int gen_vsites_tyr(gpp_atomtype_t atype, rvec *newx[],
1137 t_atom *newatom[], char ***newatomname[],
1138 int *o2n[], int *newvsite_type[], int *newcgnr[],
1139 t_symtab *symtab, int *nadd, rvec x[], int *cgnr[],
1140 t_atoms *at, int *vsite_type[], t_params plist[],
1141 int nrfound, int *ats, int add_shift,
1142 t_vsitetop *vsitetop, int nvsitetop)
1144 int nvsite, i, i0, j, atM, tpM;
1145 real dCGCE, dCEOH, dCGM, tmp1, a, b;
1146 real bond_cc, bond_ch, bond_co, bond_oh, angle_coh;
1148 real vmass, vdist, mM;
1152 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
1154 atCG, atCD1, atHD1, atCD2, atHD2, atCE1, atHE1, atCE2, atHE2,
1155 atCZ, atOH, atHH, atNR
1157 real xi[atNR], yi[atNR];
1158 /* CG, CE1, CE2 (as in general 6-ring) and OH and HH stay,
1159 rest gets virtualized.
1160 Now we have two linked triangles with one improper keeping them flat */
1161 if (atNR != nrfound)
1163 gmx_incons("Number of atom types in gen_vsites_tyr");
1166 /* Aromatic rings have 6-fold symmetry, so we only need one bond length
1167 * for the ring part (angle is always 120 degrees).
1169 bond_cc = get_ddb_bond(vsitetop, nvsitetop, "TYR", "CD1", "CE1");
1170 bond_ch = get_ddb_bond(vsitetop, nvsitetop, "TYR", "CD1", "HD1");
1171 bond_co = get_ddb_bond(vsitetop, nvsitetop, "TYR", "CZ", "OH");
1172 bond_oh = get_ddb_bond(vsitetop, nvsitetop, "TYR", "OH", "HH");
1173 angle_coh = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, "TYR", "CZ", "OH", "HH");
1175 xi[atCG] = -bond_cc+bond_cc*cos(ANGLE_6RING);
1177 xi[atCD1] = -bond_cc;
1178 yi[atCD1] = bond_cc*sin(0.5*ANGLE_6RING);
1179 xi[atHD1] = xi[atCD1]+bond_ch*cos(ANGLE_6RING);
1180 yi[atHD1] = yi[atCD1]+bond_ch*sin(ANGLE_6RING);
1182 yi[atCE1] = yi[atCD1];
1183 xi[atHE1] = xi[atCE1]-bond_ch*cos(ANGLE_6RING);
1184 yi[atHE1] = yi[atCE1]+bond_ch*sin(ANGLE_6RING);
1185 xi[atCD2] = xi[atCD1];
1186 yi[atCD2] = -yi[atCD1];
1187 xi[atHD2] = xi[atHD1];
1188 yi[atHD2] = -yi[atHD1];
1189 xi[atCE2] = xi[atCE1];
1190 yi[atCE2] = -yi[atCE1];
1191 xi[atHE2] = xi[atHE1];
1192 yi[atHE2] = -yi[atHE1];
1193 xi[atCZ] = bond_cc*cos(0.5*ANGLE_6RING);
1195 xi[atOH] = xi[atCZ]+bond_co;
1199 for (i = 0; i < atOH; i++)
1201 xcom += xi[i]*at->atom[ats[i]].m;
1202 mtot += at->atom[ats[i]].m;
1206 /* first do 6 ring as default,
1207 except CZ (we'll do that different) and HZ (we don't have that): */
1208 nvsite = gen_vsites_6ring(at, vsite_type, plist, nrfound, ats, bond_cc, bond_ch, xcom, FALSE);
1210 /* then construct CZ from the 2nd triangle */
1211 /* vsite3 construction: r_d = r_i + a r_ij + b r_ik */
1212 a = b = 0.5 * bond_co / ( bond_co - bond_cc*cos(ANGLE_6RING) );
1213 add_vsite3_param(&plist[F_VSITE3],
1214 ats[atCZ], ats[atOH], ats[atCE1], ats[atCE2], a, b);
1215 at->atom[ats[atCZ]].m = at->atom[ats[atCZ]].mB = 0;
1217 /* constraints between CE1, CE2 and OH */
1218 dCGCE = sqrt( cosrule(bond_cc, bond_cc, ANGLE_6RING) );
1219 dCEOH = sqrt( cosrule(bond_cc, bond_co, ANGLE_6RING) );
1220 my_add_param(&(plist[F_CONSTRNC]), ats[atCE1], ats[atOH], dCEOH);
1221 my_add_param(&(plist[F_CONSTRNC]), ats[atCE2], ats[atOH], dCEOH);
1223 /* We also want to constrain the angle C-O-H, but since CZ is constructed
1224 * we need to introduce a constraint to CG.
1225 * CG is much further away, so that will lead to instabilities in LINCS
1226 * when we constrain both CG-HH and OH-HH distances. Instead of requiring
1227 * the use of lincs_order=8 we introduce a dummy mass three times further
1228 * away from OH than HH. The mass is accordingly a third, with the remaining
1229 * 2/3 moved to OH. This shouldnt cause any problems since the forces will
1230 * apply to the HH constructed atom and not directly on the virtual mass.
1233 vdist = 2.0*bond_oh;
1234 mM = at->atom[ats[atHH]].m/2.0;
1235 at->atom[ats[atOH]].m += mM; /* add 1/2 of original H mass */
1236 at->atom[ats[atOH]].mB += mM; /* add 1/2 of original H mass */
1237 at->atom[ats[atHH]].m = at->atom[ats[atHH]].mB = 0;
1239 /* get dummy mass type */
1240 tpM = vsite_nm2type("MW", atype);
1241 /* make space for 1 mass: shift HH only */
1246 fprintf(stderr, "Inserting 1 dummy mass at %d\n", (*o2n)[i0]+1);
1249 for (j = i0; j < at->nr; j++)
1251 (*o2n)[j] = j+*nadd;
1253 srenew(*newx, at->nr+*nadd);
1254 srenew(*newatom, at->nr+*nadd);
1255 srenew(*newatomname, at->nr+*nadd);
1256 srenew(*newvsite_type, at->nr+*nadd);
1257 srenew(*newcgnr, at->nr+*nadd);
1258 (*newatomname)[at->nr+*nadd-1] = NULL;
1260 /* Calc the dummy mass initial position */
1261 rvec_sub(x[ats[atHH]], x[ats[atOH]], r1);
1263 rvec_add(r1, x[ats[atHH]], (*newx)[atM]);
1265 strcpy(name, "MW1");
1266 (*newatomname) [atM] = put_symtab(symtab, name);
1267 (*newatom) [atM].m = (*newatom)[atM].mB = mM;
1268 (*newatom) [atM].q = (*newatom)[atM].qB = 0.0;
1269 (*newatom) [atM].type = (*newatom)[atM].typeB = tpM;
1270 (*newatom) [atM].ptype = eptAtom;
1271 (*newatom) [atM].resind = at->atom[i0].resind;
1272 (*newatom) [atM].elem[0] = 'M';
1273 (*newatom) [atM].elem[1] = '\0';
1274 (*newvsite_type)[atM] = NOTSET;
1275 (*newcgnr) [atM] = (*cgnr)[i0];
1276 /* renumber cgnr: */
1277 for (i = i0; i < at->nr; i++)
1282 (*vsite_type)[ats[atHH]] = F_VSITE2;
1284 /* assume we also want the COH angle constrained: */
1285 tmp1 = bond_cc*cos(0.5*ANGLE_6RING) + dCGCE*sin(ANGLE_6RING*0.5) + bond_co;
1286 dCGM = sqrt( cosrule(tmp1, vdist, angle_coh) );
1287 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], add_shift+atM, dCGM);
1288 my_add_param(&(plist[F_CONSTRNC]), ats[atOH], add_shift+atM, vdist);
1290 add_vsite2_param(&plist[F_VSITE2],
1291 ats[atHH], ats[atOH], add_shift+atM, 1.0/2.0);
1295 static int gen_vsites_his(t_atoms *at, int *vsite_type[], t_params plist[],
1296 int nrfound, int *ats, t_vsitetop *vsitetop, int nvsitetop)
1299 real a, b, alpha, dCGCE1, dCGNE2;
1300 real sinalpha, cosalpha;
1301 real xcom, ycom, mtot;
1302 real mG, mrest, mCE1, mNE2;
1303 real b_CG_ND1, b_ND1_CE1, b_CE1_NE2, b_CG_CD2, b_CD2_NE2;
1304 real b_ND1_HD1, b_NE2_HE2, b_CE1_HE1, b_CD2_HD2;
1305 real a_CG_ND1_CE1, a_CG_CD2_NE2, a_ND1_CE1_NE2, a_CE1_NE2_CD2;
1306 real a_NE2_CE1_HE1, a_NE2_CD2_HD2, a_CE1_ND1_HD1, a_CE1_NE2_HE2;
1309 /* these MUST correspond to the atnms array in do_vsite_aromatics! */
1311 atCG, atND1, atHD1, atCD2, atHD2, atCE1, atHE1, atNE2, atHE2, atNR
1313 real x[atNR], y[atNR];
1315 /* CG, CE1 and NE2 stay, each gets part of the total mass,
1316 rest gets virtualized */
1317 /* check number of atoms, 3 hydrogens may be missing: */
1318 /* assert( nrfound >= atNR-3 || nrfound <= atNR );
1319 * Don't understand the above logic. Shouldn't it be && rather than || ???
1321 if ((nrfound < atNR-3) || (nrfound > atNR))
1323 gmx_incons("Generating vsites for HIS");
1326 /* avoid warnings about uninitialized variables */
1327 b_ND1_HD1 = b_NE2_HE2 = b_CE1_HE1 = b_CD2_HD2 = a_NE2_CE1_HE1 =
1328 a_NE2_CD2_HD2 = a_CE1_ND1_HD1 = a_CE1_NE2_HE2 = 0;
1330 if (ats[atHD1] != NOTSET)
1332 if (ats[atHE2] != NOTSET)
1334 sprintf(resname, "HISH");
1338 sprintf(resname, "HISA");
1343 sprintf(resname, "HISB");
1346 /* Get geometry from database */
1347 b_CG_ND1 = get_ddb_bond(vsitetop, nvsitetop, resname, "CG", "ND1");
1348 b_ND1_CE1 = get_ddb_bond(vsitetop, nvsitetop, resname, "ND1", "CE1");
1349 b_CE1_NE2 = get_ddb_bond(vsitetop, nvsitetop, resname, "CE1", "NE2");
1350 b_CG_CD2 = get_ddb_bond(vsitetop, nvsitetop, resname, "CG", "CD2");
1351 b_CD2_NE2 = get_ddb_bond(vsitetop, nvsitetop, resname, "CD2", "NE2");
1352 a_CG_ND1_CE1 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "CG", "ND1", "CE1");
1353 a_CG_CD2_NE2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "CG", "CD2", "NE2");
1354 a_ND1_CE1_NE2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "ND1", "CE1", "NE2");
1355 a_CE1_NE2_CD2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "CE1", "NE2", "CD2");
1357 if (ats[atHD1] != NOTSET)
1359 b_ND1_HD1 = get_ddb_bond(vsitetop, nvsitetop, resname, "ND1", "HD1");
1360 a_CE1_ND1_HD1 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "CE1", "ND1", "HD1");
1362 if (ats[atHE2] != NOTSET)
1364 b_NE2_HE2 = get_ddb_bond(vsitetop, nvsitetop, resname, "NE2", "HE2");
1365 a_CE1_NE2_HE2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "CE1", "NE2", "HE2");
1367 if (ats[atHD2] != NOTSET)
1369 b_CD2_HD2 = get_ddb_bond(vsitetop, nvsitetop, resname, "CD2", "HD2");
1370 a_NE2_CD2_HD2 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "NE2", "CD2", "HD2");
1372 if (ats[atHE1] != NOTSET)
1374 b_CE1_HE1 = get_ddb_bond(vsitetop, nvsitetop, resname, "CE1", "HE1");
1375 a_NE2_CE1_HE1 = DEG2RAD*get_ddb_angle(vsitetop, nvsitetop, resname, "NE2", "CE1", "HE1");
1378 /* constraints between CG, CE1 and NE1 */
1379 dCGCE1 = sqrt( cosrule(b_CG_ND1, b_ND1_CE1, a_CG_ND1_CE1) );
1380 dCGNE2 = sqrt( cosrule(b_CG_CD2, b_CD2_NE2, a_CG_CD2_NE2) );
1382 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atCE1], dCGCE1);
1383 my_add_param(&(plist[F_CONSTRNC]), ats[atCG], ats[atNE2], dCGNE2);
1384 /* we already have a constraint CE1-NE2, so we don't add it again */
1386 /* calculate the positions in a local frame of reference.
1387 * The x-axis is the line from CG that makes a right angle
1388 * with the bond CE1-NE2, and the y-axis the bond CE1-NE2.
1390 /* First calculate the x-axis intersection with y-axis (=yCE1).
1391 * Get cos(angle CG-CE1-NE2) :
1393 cosalpha = acosrule(dCGNE2, dCGCE1, b_CE1_NE2);
1395 y[atCE1] = cosalpha*dCGCE1;
1397 y[atNE2] = y[atCE1]-b_CE1_NE2;
1398 sinalpha = sqrt(1-cosalpha*cosalpha);
1399 x[atCG] = -sinalpha*dCGCE1;
1401 x[atHE1] = x[atHE2] = x[atHD1] = x[atHD2] = 0;
1402 y[atHE1] = y[atHE2] = y[atHD1] = y[atHD2] = 0;
1404 /* calculate ND1 and CD2 positions from CE1 and NE2 */
1406 x[atND1] = -b_ND1_CE1*sin(a_ND1_CE1_NE2);
1407 y[atND1] = y[atCE1]-b_ND1_CE1*cos(a_ND1_CE1_NE2);
1409 x[atCD2] = -b_CD2_NE2*sin(a_CE1_NE2_CD2);
1410 y[atCD2] = y[atNE2]+b_CD2_NE2*cos(a_CE1_NE2_CD2);
1412 /* And finally the hydrogen positions */
1413 if (ats[atHE1] != NOTSET)
1415 x[atHE1] = x[atCE1] + b_CE1_HE1*sin(a_NE2_CE1_HE1);
1416 y[atHE1] = y[atCE1] - b_CE1_HE1*cos(a_NE2_CE1_HE1);
1418 /* HD2 - first get (ccw) angle from (positive) y-axis */
1419 if (ats[atHD2] != NOTSET)
1421 alpha = a_CE1_NE2_CD2 + M_PI - a_NE2_CD2_HD2;
1422 x[atHD2] = x[atCD2] - b_CD2_HD2*sin(alpha);
1423 y[atHD2] = y[atCD2] + b_CD2_HD2*cos(alpha);
1425 if (ats[atHD1] != NOTSET)
1427 /* HD1 - first get (cw) angle from (positive) y-axis */
1428 alpha = a_ND1_CE1_NE2 + M_PI - a_CE1_ND1_HD1;
1429 x[atHD1] = x[atND1] - b_ND1_HD1*sin(alpha);
1430 y[atHD1] = y[atND1] - b_ND1_HD1*cos(alpha);
1432 if (ats[atHE2] != NOTSET)
1434 x[atHE2] = x[atNE2] + b_NE2_HE2*sin(a_CE1_NE2_HE2);
1435 y[atHE2] = y[atNE2] + b_NE2_HE2*cos(a_CE1_NE2_HE2);
1437 /* Have all coordinates now */
1439 /* calc center-of-mass; keep atoms CG, CE1, NE2 and
1440 * set the rest to vsite3
1442 mtot = xcom = ycom = 0;
1444 for (i = 0; i < atNR; i++)
1446 if (ats[i] != NOTSET)
1448 mtot += at->atom[ats[i]].m;
1449 xcom += x[i]*at->atom[ats[i]].m;
1450 ycom += y[i]*at->atom[ats[i]].m;
1451 if (i != atCG && i != atCE1 && i != atNE2)
1453 at->atom[ats[i]].m = at->atom[ats[i]].mB = 0;
1454 (*vsite_type)[ats[i]] = F_VSITE3;
1459 if (nvsite+3 != nrfound)
1461 gmx_incons("Generating vsites for HIS");
1467 /* distribute mass so that com stays the same */
1468 mG = xcom*mtot/x[atCG];
1470 mCE1 = (ycom-y[atNE2])*mrest/(y[atCE1]-y[atNE2]);
1473 at->atom[ats[atCG]].m = at->atom[ats[atCG]].mB = mG;
1474 at->atom[ats[atCE1]].m = at->atom[ats[atCE1]].mB = mCE1;
1475 at->atom[ats[atNE2]].m = at->atom[ats[atNE2]].mB = mNE2;
1478 if (ats[atHE1] != NOTSET)
1480 calc_vsite3_param(x[atHE1], y[atHE1], x[atCE1], y[atCE1], x[atNE2], y[atNE2],
1481 x[atCG], y[atCG], &a, &b);
1482 add_vsite3_param(&plist[F_VSITE3],
1483 ats[atHE1], ats[atCE1], ats[atNE2], ats[atCG], a, b);
1486 if (ats[atHE2] != NOTSET)
1488 calc_vsite3_param(x[atHE2], y[atHE2], x[atNE2], y[atNE2], x[atCE1], y[atCE1],
1489 x[atCG], y[atCG], &a, &b);
1490 add_vsite3_param(&plist[F_VSITE3],
1491 ats[atHE2], ats[atNE2], ats[atCE1], ats[atCG], a, b);
1495 calc_vsite3_param(x[atND1], y[atND1], x[atNE2], y[atNE2], x[atCE1], y[atCE1],
1496 x[atCG], y[atCG], &a, &b);
1497 add_vsite3_param(&plist[F_VSITE3],
1498 ats[atND1], ats[atNE2], ats[atCE1], ats[atCG], a, b);
1501 calc_vsite3_param(x[atCD2], y[atCD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2],
1502 x[atCG], y[atCG], &a, &b);
1503 add_vsite3_param(&plist[F_VSITE3],
1504 ats[atCD2], ats[atCE1], ats[atNE2], ats[atCG], a, b);
1507 if (ats[atHD1] != NOTSET)
1509 calc_vsite3_param(x[atHD1], y[atHD1], x[atNE2], y[atNE2], x[atCE1], y[atCE1],
1510 x[atCG], y[atCG], &a, &b);
1511 add_vsite3_param(&plist[F_VSITE3],
1512 ats[atHD1], ats[atNE2], ats[atCE1], ats[atCG], a, b);
1515 if (ats[atHD2] != NOTSET)
1517 calc_vsite3_param(x[atHD2], y[atHD2], x[atCE1], y[atCE1], x[atNE2], y[atNE2],
1518 x[atCG], y[atCG], &a, &b);
1519 add_vsite3_param(&plist[F_VSITE3],
1520 ats[atHD2], ats[atCE1], ats[atNE2], ats[atCG], a, b);
1525 static gmx_bool is_vsite(int vsite_type)
1527 if (vsite_type == NOTSET)
1531 switch (abs(vsite_type) )
1545 static char atomnamesuffix[] = "1234";
1547 void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
1548 t_atoms *at, t_symtab *symtab, rvec *x[],
1549 t_params plist[], int *vsite_type[], int *cgnr[],
1550 real mHmult, gmx_bool bVsiteAromatics,
1553 #define MAXATOMSPERRESIDUE 16
1554 int i, j, k, m, i0, ni0, whatres, resind, add_shift, ftype, nvsite, nadd;
1556 int nrfound = 0, needed, nrbonds, nrHatoms, Heavy, nrheavies, tpM, tpHeavy;
1557 int Hatoms[4], heavies[4], bb;
1558 gmx_bool bWARNING, bAddVsiteParam, bFirstWater;
1560 gmx_bool *bResProcessed;
1561 real mHtot, mtot, fact, fact2;
1562 rvec rpar, rperp, temp;
1563 char name[10], tpname[32], nexttpname[32], *ch;
1565 int *o2n, *newvsite_type, *newcgnr, ats[MAXATOMSPERRESIDUE];
1568 char ***newatomname;
1572 int nvsiteconf, nvsitetop, cmplength;
1573 gmx_bool isN, planarN, bFound;
1574 gmx_residuetype_t rt;
1576 t_vsiteconf *vsiteconflist;
1577 /* pointer to a list of CH3/NH3/NH2 configuration entries.
1578 * See comments in read_vsite_database. It isnt beautiful,
1579 * but it had to be fixed, and I dont even want to try to
1580 * maintain this part of the code...
1582 t_vsitetop *vsitetop;
1583 /* Pointer to a list of geometry (bond/angle) entries for
1584 * residues like PHE, TRP, TYR, HIS, etc., where we need
1585 * to know the geometry to construct vsite aromatics.
1586 * Note that equilibrium geometry isnt necessarily the same
1587 * as the individual bond and angle values given in the
1588 * force field (rings can be strained).
1591 /* if bVsiteAromatics=TRUE do_vsites will specifically convert atoms in
1592 PHE, TRP, TYR and HIS to a construction of virtual sites */
1594 resPHE, resTRP, resTYR, resHIS, resNR
1596 const char *resnms[resNR] = { "PHE", "TRP", "TYR", "HIS" };
1597 /* Amber03 alternative names for termini */
1598 const char *resnmsN[resNR] = { "NPHE", "NTRP", "NTYR", "NHIS" };
1599 const char *resnmsC[resNR] = { "CPHE", "CTRP", "CTYR", "CHIS" };
1600 /* HIS can be known as HISH, HIS1, HISA, HID, HIE, HIP, etc. too */
1601 gmx_bool bPartial[resNR] = { FALSE, FALSE, FALSE, TRUE };
1602 /* the atnms for every residue MUST correspond to the enums in the
1603 gen_vsites_* (one for each residue) routines! */
1604 /* also the atom names in atnms MUST be in the same order as in the .rtp! */
1605 const char *atnms[resNR][MAXATOMSPERRESIDUE+1] = {
1607 "CD1", "HD1", "CD2", "HD2",
1608 "CE1", "HE1", "CE2", "HE2",
1612 "CD1", "HD1", "CD2",
1613 "NE1", "HE1", "CE2", "CE3", "HE3",
1614 "CZ2", "HZ2", "CZ3", "HZ3",
1615 "CH2", "HH2", NULL },
1617 "CD1", "HD1", "CD2", "HD2",
1618 "CE1", "HE1", "CE2", "HE2",
1619 "CZ", "OH", "HH", NULL },
1621 "ND1", "HD1", "CD2", "HD2",
1622 "CE1", "HE1", "NE2", "HE2", NULL }
1627 printf("Searching for atoms to make virtual sites ...\n");
1628 fprintf(debug, "# # # VSITES # # #\n");
1631 ndb = fflib_search_file_end(ffdir, ".vsd", FALSE, &db);
1633 vsiteconflist = NULL;
1636 for (f = 0; f < ndb; f++)
1638 read_vsite_database(db[f], &vsiteconflist, &nvsiteconf, &vsitetop, &nvsitetop);
1646 /* we need a marker for which atoms should *not* be renumbered afterwards */
1647 add_shift = 10*at->nr;
1648 /* make arrays where masses can be inserted into */
1650 snew(newatom, at->nr);
1651 snew(newatomname, at->nr);
1652 snew(newvsite_type, at->nr);
1653 snew(newcgnr, at->nr);
1654 /* make index array to tell where the atoms go to when masses are inserted */
1656 for (i = 0; i < at->nr; i++)
1660 /* make index to tell which residues were already processed */
1661 snew(bResProcessed, at->nres);
1663 gmx_residuetype_init(&rt);
1665 /* generate vsite constructions */
1666 /* loop over all atoms */
1668 for (i = 0; (i < at->nr); i++)
1670 if (at->atom[i].resind != resind)
1672 resind = at->atom[i].resind;
1673 resnm = *(at->resinfo[resind].name);
1675 /* first check for aromatics to virtualize */
1676 /* don't waste our effort on DNA, water etc. */
1677 /* Only do the vsite aromatic stuff when we reach the
1678 * CA atom, since there might be an X2/X3 group on the
1679 * N-terminus that must be treated first.
1681 if (bVsiteAromatics &&
1682 !strcmp(*(at->atomname[i]), "CA") &&
1683 !bResProcessed[resind] &&
1684 gmx_residuetype_is_protein(rt, *(at->resinfo[resind].name)) )
1686 /* mark this residue */
1687 bResProcessed[resind] = TRUE;
1688 /* find out if this residue needs converting */
1690 for (j = 0; j < resNR && whatres == NOTSET; j++)
1693 cmplength = bPartial[j] ? strlen(resnm)-1 : strlen(resnm);
1695 bFound = ((gmx_strncasecmp(resnm, resnms[j], cmplength) == 0) ||
1696 (gmx_strncasecmp(resnm, resnmsN[j], cmplength) == 0) ||
1697 (gmx_strncasecmp(resnm, resnmsC[j], cmplength) == 0));
1702 /* get atoms we will be needing for the conversion */
1704 for (k = 0; atnms[j][k]; k++)
1707 for (m = i; m < at->nr && at->atom[m].resind == resind && ats[k] == NOTSET; m++)
1709 if (gmx_strcasecmp(*(at->atomname[m]), atnms[j][k]) == 0)
1717 /* now k is number of atom names in atnms[j] */
1726 if (nrfound < needed)
1728 gmx_fatal(FARGS, "not enough atoms found (%d, need %d) in "
1729 "residue %s %d while\n "
1730 "generating aromatics virtual site construction",
1731 nrfound, needed, resnm, at->resinfo[resind].nr);
1733 /* Advance overall atom counter */
1737 /* the enums for every residue MUST correspond to atnms[residue] */
1743 fprintf(stderr, "PHE at %d\n", o2n[ats[0]]+1);
1745 nvsite += gen_vsites_phe(at, vsite_type, plist, nrfound, ats, vsitetop, nvsitetop);
1750 fprintf(stderr, "TRP at %d\n", o2n[ats[0]]+1);
1752 nvsite += gen_vsites_trp(atype, &newx, &newatom, &newatomname, &o2n,
1753 &newvsite_type, &newcgnr, symtab, &nadd, *x, cgnr,
1754 at, vsite_type, plist, nrfound, ats, add_shift, vsitetop, nvsitetop);
1759 fprintf(stderr, "TYR at %d\n", o2n[ats[0]]+1);
1761 nvsite += gen_vsites_tyr(atype, &newx, &newatom, &newatomname, &o2n,
1762 &newvsite_type, &newcgnr, symtab, &nadd, *x, cgnr,
1763 at, vsite_type, plist, nrfound, ats, add_shift, vsitetop, nvsitetop);
1768 fprintf(stderr, "HIS at %d\n", o2n[ats[0]]+1);
1770 nvsite += gen_vsites_his(at, vsite_type, plist, nrfound, ats, vsitetop, nvsitetop);
1773 /* this means this residue won't be processed */
1776 gmx_fatal(FARGS, "DEATH HORROR in do_vsites (%s:%d)",
1777 __FILE__, __LINE__);
1778 } /* switch whatres */
1779 /* skip back to beginning of residue */
1780 while (i > 0 && at->atom[i-1].resind == resind)
1784 } /* if bVsiteAromatics & is protein */
1786 /* now process the rest of the hydrogens */
1787 /* only process hydrogen atoms which are not already set */
1788 if ( ((*vsite_type)[i] == NOTSET) && is_hydrogen(*(at->atomname[i])))
1790 /* find heavy atom, count #bonds from it and #H atoms bound to it
1791 and return H atom numbers (Hatoms) and heavy atom numbers (heavies) */
1792 count_bonds(i, &plist[F_BONDS], at->atomname,
1793 &nrbonds, &nrHatoms, Hatoms, &Heavy, &nrheavies, heavies);
1794 /* get Heavy atom type */
1795 tpHeavy = get_atype(Heavy, at, nrtp, rtp, rt);
1796 strcpy(tpname, get_atomtype_name(tpHeavy, atype));
1799 bAddVsiteParam = TRUE;
1800 /* nested if's which check nrHatoms, nrbonds and atomname */
1806 (*vsite_type)[i] = F_BONDS;
1808 case 3: /* =CH-, -NH- or =NH+- */
1809 (*vsite_type)[i] = F_VSITE3FD;
1811 case 4: /* --CH- (tert) */
1812 /* The old type 4FD had stability issues, so
1813 * all new constructs should use 4FDN
1815 (*vsite_type)[i] = F_VSITE4FDN;
1817 /* Check parity of heavy atoms from coordinates */
1822 rvec_sub((*x)[aj], (*x)[ai], tmpmat[0]);
1823 rvec_sub((*x)[ak], (*x)[ai], tmpmat[1]);
1824 rvec_sub((*x)[al], (*x)[ai], tmpmat[2]);
1826 if (det(tmpmat) > 0)
1834 default: /* nrbonds != 2, 3 or 4 */
1839 else if ( /*(nrHatoms == 2) && (nrbonds == 2) && REMOVED this test
1841 (gmx_strncasecmp(*at->atomname[Heavy], "OW", 2) == 0) )
1843 bAddVsiteParam = FALSE; /* this is water: skip these hydrogens */
1846 bFirstWater = FALSE;
1850 "Not converting hydrogens in water to virtual sites\n");
1854 else if ( (nrHatoms == 2) && (nrbonds == 4) )
1856 /* -CH2- , -NH2+- */
1857 (*vsite_type)[Hatoms[0]] = F_VSITE3OUT;
1858 (*vsite_type)[Hatoms[1]] = -F_VSITE3OUT;
1862 /* 2 or 3 hydrogen atom, with 3 or 4 bonds in total to the heavy atom.
1863 * If it is a nitrogen, first check if it is planar.
1865 isN = planarN = FALSE;
1866 if ((nrHatoms == 2) && ((*at->atomname[Heavy])[0] == 'N'))
1869 j = nitrogen_is_planar(vsiteconflist, nvsiteconf, tpname);
1872 gmx_fatal(FARGS, "No vsite database NH2 entry for type %s\n", tpname);
1876 if ( (nrHatoms == 2) && (nrbonds == 3) && ( !isN || planarN ) )
1878 /* =CH2 or, if it is a nitrogen NH2, it is a planar one */
1879 (*vsite_type)[Hatoms[0]] = F_VSITE3FAD;
1880 (*vsite_type)[Hatoms[1]] = -F_VSITE3FAD;
1882 else if ( ( (nrHatoms == 2) && (nrbonds == 3) &&
1883 ( isN && !planarN ) ) ||
1884 ( (nrHatoms == 3) && (nrbonds == 4) ) )
1886 /* CH3, NH3 or non-planar NH2 group */
1887 int Hat_vsite_type[3] = { F_VSITE3, F_VSITE3OUT, F_VSITE3OUT };
1888 gmx_bool Hat_SwapParity[3] = { FALSE, TRUE, FALSE };
1892 fprintf(stderr, "-XH3 or nonplanar NH2 group at %d\n", i+1);
1894 bAddVsiteParam = FALSE; /* we'll do this ourselves! */
1895 /* -NH2 (umbrella), -NH3+ or -CH3 */
1896 (*vsite_type)[Heavy] = F_VSITE3;
1897 for (j = 0; j < nrHatoms; j++)
1899 (*vsite_type)[Hatoms[j]] = Hat_vsite_type[j];
1901 /* get dummy mass type from first char of heavy atom type (N or C) */
1903 strcpy(nexttpname, get_atomtype_name(get_atype(heavies[0], at, nrtp, rtp, rt), atype));
1904 ch = get_dummymass_name(vsiteconflist, nvsiteconf, tpname, nexttpname);
1910 gmx_fatal(FARGS, "Can't find dummy mass for type %s bonded to type %s in the virtual site database (.vsd files). Add it to the database!\n", tpname, nexttpname);
1914 gmx_fatal(FARGS, "A dummy mass for type %s bonded to type %s is required, but no virtual site database (.vsd) files where found.\n", tpname, nexttpname);
1922 tpM = vsite_nm2type(name, atype);
1923 /* make space for 2 masses: shift all atoms starting with 'Heavy' */
1929 fprintf(stderr, "Inserting %d dummy masses at %d\n", NMASS, o2n[i0]+1);
1932 for (j = i0; j < at->nr; j++)
1937 srenew(newx, at->nr+nadd);
1938 srenew(newatom, at->nr+nadd);
1939 srenew(newatomname, at->nr+nadd);
1940 srenew(newvsite_type, at->nr+nadd);
1941 srenew(newcgnr, at->nr+nadd);
1943 for (j = 0; j < NMASS; j++)
1945 newatomname[at->nr+nadd-1-j] = NULL;
1948 /* calculate starting position for the masses */
1950 /* get atom masses, and set Heavy and Hatoms mass to zero */
1951 for (j = 0; j < nrHatoms; j++)
1953 mHtot += get_amass(Hatoms[j], at, nrtp, rtp, rt);
1954 at->atom[Hatoms[j]].m = at->atom[Hatoms[j]].mB = 0;
1956 mtot = mHtot + get_amass(Heavy, at, nrtp, rtp, rt);
1957 at->atom[Heavy].m = at->atom[Heavy].mB = 0;
1964 /* generate vectors parallel and perpendicular to rotational axis:
1965 * rpar = Heavy -> Hcom
1966 * rperp = Hcom -> H1 */
1968 for (j = 0; j < nrHatoms; j++)
1970 rvec_inc(rpar, (*x)[Hatoms[j]]);
1972 svmul(1.0/nrHatoms, rpar, rpar); /* rpar = ( H1+H2+H3 ) / 3 */
1973 rvec_dec(rpar, (*x)[Heavy]); /* - Heavy */
1974 rvec_sub((*x)[Hatoms[0]], (*x)[Heavy], rperp);
1975 rvec_dec(rperp, rpar); /* rperp = H1 - Heavy - rpar */
1976 /* calc mass positions */
1977 svmul(fact2, rpar, temp);
1978 for (j = 0; (j < NMASS); j++) /* xM = xN + fact2 * rpar +/- fact * rperp */
1980 rvec_add((*x)[Heavy], temp, newx[ni0+j]);
1982 svmul(fact, rperp, temp);
1983 rvec_inc(newx[ni0 ], temp);
1984 rvec_dec(newx[ni0+1], temp);
1985 /* set atom parameters for the masses */
1986 for (j = 0; (j < NMASS); j++)
1988 /* make name: "M??#" or "M?#" (? is atomname, # is number) */
1990 for (k = 0; (*at->atomname[Heavy])[k] && ( k < NMASS ); k++)
1992 name[k+1] = (*at->atomname[Heavy])[k];
1994 name[k+1] = atomnamesuffix[j];
1996 newatomname[ni0+j] = put_symtab(symtab, name);
1997 newatom[ni0+j].m = newatom[ni0+j].mB = mtot/NMASS;
1998 newatom[ni0+j].q = newatom[ni0+j].qB = 0.0;
1999 newatom[ni0+j].type = newatom[ni0+j].typeB = tpM;
2000 newatom[ni0+j].ptype = eptAtom;
2001 newatom[ni0+j].resind = at->atom[i0].resind;
2002 newatom[ni0+j].elem[0] = 'M';
2003 newatom[ni0+j].elem[1] = '\0';
2004 newvsite_type[ni0+j] = NOTSET;
2005 newcgnr[ni0+j] = (*cgnr)[i0];
2007 /* add constraints between dummy masses and to heavies[0] */
2008 /* 'add_shift' says which atoms won't be renumbered afterwards */
2009 my_add_param(&(plist[F_CONSTRNC]), heavies[0], add_shift+ni0, NOTSET);
2010 my_add_param(&(plist[F_CONSTRNC]), heavies[0], add_shift+ni0+1, NOTSET);
2011 my_add_param(&(plist[F_CONSTRNC]), add_shift+ni0, add_shift+ni0+1, NOTSET);
2013 /* generate Heavy, H1, H2 and H3 from M1, M2 and heavies[0] */
2014 /* note that vsite_type cannot be NOTSET, because we just set it */
2015 add_vsite3_atoms (&plist[(*vsite_type)[Heavy]],
2016 Heavy, heavies[0], add_shift+ni0, add_shift+ni0+1,
2018 for (j = 0; j < nrHatoms; j++)
2020 add_vsite3_atoms(&plist[(*vsite_type)[Hatoms[j]]],
2021 Hatoms[j], heavies[0], add_shift+ni0, add_shift+ni0+1,
2035 "Warning: cannot convert atom %d %s (bound to a heavy atom "
2037 " %d bonds and %d bound hydrogens atoms) to virtual site\n",
2038 i+1, *(at->atomname[i]), tpname, nrbonds, nrHatoms);
2042 /* add vsite parameters to topology,
2043 also get rid of negative vsite_types */
2044 add_vsites(plist, (*vsite_type), Heavy, nrHatoms, Hatoms,
2045 nrheavies, heavies);
2046 /* transfer mass of virtual site to Heavy atom */
2047 for (j = 0; j < nrHatoms; j++)
2049 if (is_vsite((*vsite_type)[Hatoms[j]]))
2051 at->atom[Heavy].m += at->atom[Hatoms[j]].m;
2052 at->atom[Heavy].mB = at->atom[Heavy].m;
2053 at->atom[Hatoms[j]].m = at->atom[Hatoms[j]].mB = 0;
2060 fprintf(debug, "atom %d: ", o2n[i]+1);
2061 print_bonds(debug, o2n, nrHatoms, Hatoms, Heavy, nrheavies, heavies);
2063 } /* if vsite NOTSET & is hydrogen */
2065 } /* for i < at->nr */
2067 gmx_residuetype_destroy(rt);
2071 fprintf(debug, "Before inserting new atoms:\n");
2072 for (i = 0; i < at->nr; i++)
2074 fprintf(debug, "%4d %4d %4s %4d %4s %6d %-10s\n", i+1, o2n[i]+1,
2075 at->atomname[i] ? *(at->atomname[i]) : "(NULL)",
2076 at->resinfo[at->atom[i].resind].nr,
2077 at->resinfo[at->atom[i].resind].name ?
2078 *(at->resinfo[at->atom[i].resind].name) : "(NULL)",
2080 ((*vsite_type)[i] == NOTSET) ?
2081 "NOTSET" : interaction_function[(*vsite_type)[i]].name);
2083 fprintf(debug, "new atoms to be inserted:\n");
2084 for (i = 0; i < at->nr+nadd; i++)
2088 fprintf(debug, "%4d %4s %4d %6d %-10s\n", i+1,
2089 newatomname[i] ? *(newatomname[i]) : "(NULL)",
2090 newatom[i].resind, newcgnr[i],
2091 (newvsite_type[i] == NOTSET) ?
2092 "NOTSET" : interaction_function[newvsite_type[i]].name);
2097 /* add all original atoms to the new arrays, using o2n index array */
2098 for (i = 0; i < at->nr; i++)
2100 newatomname [o2n[i]] = at->atomname [i];
2101 newatom [o2n[i]] = at->atom [i];
2102 newvsite_type[o2n[i]] = (*vsite_type)[i];
2103 newcgnr [o2n[i]] = (*cgnr) [i];
2104 copy_rvec((*x)[i], newx[o2n[i]]);
2106 /* throw away old atoms */
2108 sfree(at->atomname);
2112 /* put in the new ones */
2115 at->atomname = newatomname;
2116 *vsite_type = newvsite_type;
2119 if (at->nr > add_shift)
2121 gmx_fatal(FARGS, "Added impossible amount of dummy masses "
2122 "(%d on a total of %d atoms)\n", nadd, at->nr-nadd);
2127 fprintf(debug, "After inserting new atoms:\n");
2128 for (i = 0; i < at->nr; i++)
2130 fprintf(debug, "%4d %4s %4d %4s %6d %-10s\n", i+1,
2131 at->atomname[i] ? *(at->atomname[i]) : "(NULL)",
2132 at->resinfo[at->atom[i].resind].nr,
2133 at->resinfo[at->atom[i].resind].name ?
2134 *(at->resinfo[at->atom[i].resind].name) : "(NULL)",
2136 ((*vsite_type)[i] == NOTSET) ?
2137 "NOTSET" : interaction_function[(*vsite_type)[i]].name);
2141 /* now renumber all the interactions because of the added atoms */
2142 for (ftype = 0; ftype < F_NRE; ftype++)
2144 params = &(plist[ftype]);
2147 fprintf(debug, "Renumbering %d %s\n", params->nr,
2148 interaction_function[ftype].longname);
2150 for (i = 0; i < params->nr; i++)
2152 for (j = 0; j < NRAL(ftype); j++)
2154 if (params->param[i].a[j] >= add_shift)
2158 fprintf(debug, " [%u -> %u]", params->param[i].a[j],
2159 params->param[i].a[j]-add_shift);
2161 params->param[i].a[j] = params->param[i].a[j]-add_shift;
2167 fprintf(debug, " [%u -> %d]", params->param[i].a[j],
2168 o2n[params->param[i].a[j]]);
2170 params->param[i].a[j] = o2n[params->param[i].a[j]];
2175 fprintf(debug, "\n");
2179 /* now check if atoms in the added constraints are in increasing order */
2180 params = &(plist[F_CONSTRNC]);
2181 for (i = 0; i < params->nr; i++)
2183 if (params->param[i].AI > params->param[i].AJ)
2185 j = params->param[i].AJ;
2186 params->param[i].AJ = params->param[i].AI;
2187 params->param[i].AI = j;
2194 /* tell the user what we did */
2195 fprintf(stderr, "Marked %d virtual sites\n", nvsite);
2196 fprintf(stderr, "Added %d dummy masses\n", nadd);
2197 fprintf(stderr, "Added %d new constraints\n", plist[F_CONSTRNC].nr);
2200 void do_h_mass(t_params *psb, int vsite_type[], t_atoms *at, real mHmult,
2201 gmx_bool bDeuterate)
2205 /* loop over all atoms */
2206 for (i = 0; i < at->nr; i++)
2208 /* adjust masses if i is hydrogen and not a virtual site */
2209 if (!is_vsite(vsite_type[i]) && is_hydrogen(*(at->atomname[i])) )
2211 /* find bonded heavy atom */
2213 for (j = 0; (j < psb->nr) && (a == NOTSET); j++)
2215 /* if other atom is not a virtual site, it is the one we want */
2216 if ( (psb->param[j].AI == i) &&
2217 !is_vsite(vsite_type[psb->param[j].AJ]) )
2219 a = psb->param[j].AJ;
2221 else if ( (psb->param[j].AJ == i) &&
2222 !is_vsite(vsite_type[psb->param[j].AI]) )
2224 a = psb->param[j].AI;
2229 gmx_fatal(FARGS, "Unbound hydrogen atom (%d) found while adjusting mass",
2233 /* adjust mass of i (hydrogen) with mHmult
2234 and correct mass of a (bonded atom) with same amount */
2237 at->atom[a].m -= (mHmult-1.0)*at->atom[i].m;
2238 at->atom[a].mB -= (mHmult-1.0)*at->atom[i].m;
2240 at->atom[i].m *= mHmult;
2241 at->atom[i].mB *= mHmult;