2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2008, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
44 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/fileio/confio.h"
46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/gmxpreprocess/gen_ad.h"
48 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
49 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
50 #include "gromacs/gmxpreprocess/grompp_impl.h"
51 #include "gromacs/gmxpreprocess/nm2type.h"
52 #include "gromacs/gmxpreprocess/notset.h"
53 #include "gromacs/gmxpreprocess/pdb2top.h"
54 #include "gromacs/gmxpreprocess/toppush.h"
55 #include "gromacs/gmxpreprocess/toputil.h"
56 #include "gromacs/listed_forces/bonded.h"
57 #include "gromacs/math/units.h"
58 #include "gromacs/math/utilities.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/math/vecdump.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/pbcutil/pbc.h"
63 #include "gromacs/topology/symtab.h"
64 #include "gromacs/topology/topology.h"
65 #include "gromacs/utility/arraysize.h"
66 #include "gromacs/utility/cstringutil.h"
67 #include "gromacs/utility/fatalerror.h"
68 #include "gromacs/utility/gmxassert.h"
69 #include "gromacs/utility/smalloc.h"
71 #include "hackblock.h"
73 #define MARGIN_FAC 1.1
75 static bool is_bond(int nnm
, t_nm2type nmt
[], char *ai
, char *aj
, real blen
)
79 for (i
= 0; (i
< nnm
); i
++)
81 for (j
= 0; (j
< nmt
[i
].nbonds
); j
++)
83 if ((((gmx_strncasecmp(ai
, nmt
[i
].elem
, 1) == 0) &&
84 (gmx_strncasecmp(aj
, nmt
[i
].bond
[j
], 1) == 0)) ||
85 ((gmx_strncasecmp(ai
, nmt
[i
].bond
[j
], 1) == 0) &&
86 (gmx_strncasecmp(aj
, nmt
[i
].elem
, 1) == 0))) &&
87 (fabs(blen
-nmt
[i
].blen
[j
]) <= 0.1*nmt
[i
].blen
[j
]))
96 static void mk_bonds(int nnm
, t_nm2type nmt
[],
97 t_atoms
*atoms
, const rvec x
[], t_params
*bond
, int nbond
[],
98 bool bPBC
, matrix box
)
106 for (i
= 0; (i
< MAXATOMLIST
); i
++)
110 for (i
= 0; (i
< MAXFORCEPARAM
); i
++)
117 set_pbc(&pbc
, -1, box
);
119 for (i
= 0; (i
< atoms
->nr
); i
++)
123 fprintf(stderr
, "\ratom %d", i
);
126 for (j
= i
+1; (j
< atoms
->nr
); j
++)
130 pbc_dx(&pbc
, x
[i
], x
[j
], dx
);
134 rvec_sub(x
[i
], x
[j
], dx
);
138 if (is_bond(nnm
, nmt
, *atoms
->atomname
[i
], *atoms
->atomname
[j
],
143 b
.c0() = std::sqrt(dx2
);
144 add_param_to_list (bond
, &b
);
150 fprintf(stderr
, "\ratom %d\n", i
);
154 static int *set_cgnr(t_atoms
*atoms
, bool bUsePDBcharge
, real
*qtot
, real
*mtot
)
161 snew(cgnr
, atoms
->nr
);
162 for (i
= 0; (i
< atoms
->nr
); i
++)
164 if (atoms
->pdbinfo
&& bUsePDBcharge
)
166 atoms
->atom
[i
].q
= atoms
->pdbinfo
[i
].bfac
;
168 qt
+= atoms
->atom
[i
].q
;
169 *qtot
+= atoms
->atom
[i
].q
;
170 *mtot
+= atoms
->atom
[i
].m
;
181 static gpp_atomtype
*set_atom_type(t_symtab
*tab
, t_atoms
*atoms
, t_params
*bonds
,
182 int *nbonds
, int nnm
, t_nm2type nm2t
[])
187 atype
= init_atomtype();
188 snew(atoms
->atomtype
, atoms
->nr
);
189 nresolved
= nm2type(nnm
, nm2t
, tab
, atoms
, atype
, nbonds
, bonds
);
190 if (nresolved
!= atoms
->nr
)
192 gmx_fatal(FARGS
, "Could only find a forcefield type for %d out of %d atoms",
193 nresolved
, atoms
->nr
);
196 fprintf(stderr
, "There are %d different atom types in your sample\n",
197 get_atomtype_ntypes(atype
));
202 static void lo_set_force_const(t_params
*plist
, real c
[], int nrfp
, bool bRound
,
203 bool bDih
, bool bParam
)
209 for (i
= 0; (i
< plist
->nr
); i
++)
213 for (j
= 0; j
< nrfp
; j
++)
222 sprintf(buf
, "%.2e", plist
->param
[i
].c
[0]);
223 sscanf(buf
, "%lf", &cc
);
228 c
[0] = plist
->param
[i
].c
[0];
233 c
[0] = (static_cast<int>(c
[0] + 3600)) % 360;
238 /* To put the minimum at the current angle rather than the maximum */
242 GMX_ASSERT(nrfp
<= MAXFORCEPARAM
/2, "Only 6 parameters may be used for an interaction");
243 for (j
= 0; (j
< nrfp
); j
++)
245 plist
->param
[i
].c
[j
] = c
[j
];
246 plist
->param
[i
].c
[nrfp
+j
] = c
[j
];
248 set_p_string(&(plist
->param
[i
]), "");
252 static void set_force_const(t_params plist
[], real kb
, real kt
, real kp
, bool bRound
,
255 real c
[MAXFORCEPARAM
];
259 lo_set_force_const(&plist
[F_BONDS
], c
, 2, bRound
, FALSE
, bParam
);
261 lo_set_force_const(&plist
[F_ANGLES
], c
, 2, bRound
, FALSE
, bParam
);
264 lo_set_force_const(&plist
[F_PDIHS
], c
, 3, bRound
, TRUE
, bParam
);
267 static void calc_angles_dihs(t_params
*ang
, t_params
*dih
, const rvec x
[], bool bPBC
,
270 int i
, ai
, aj
, ak
, al
, t1
, t2
, t3
;
271 rvec r_ij
, r_kj
, r_kl
, m
, n
;
277 set_pbc(&pbc
, epbcXYZ
, box
);
279 for (i
= 0; (i
< ang
->nr
); i
++)
281 ai
= ang
->param
[i
].ai();
282 aj
= ang
->param
[i
].aj();
283 ak
= ang
->param
[i
].ak();
284 th
= RAD2DEG
*bond_angle(x
[ai
], x
[aj
], x
[ak
], bPBC
? &pbc
: nullptr,
285 r_ij
, r_kj
, &costh
, &t1
, &t2
);
286 ang
->param
[i
].c0() = th
;
288 for (i
= 0; (i
< dih
->nr
); i
++)
290 ai
= dih
->param
[i
].ai();
291 aj
= dih
->param
[i
].aj();
292 ak
= dih
->param
[i
].ak();
293 al
= dih
->param
[i
].al();
294 ph
= RAD2DEG
*dih_angle(x
[ai
], x
[aj
], x
[ak
], x
[al
], bPBC
? &pbc
: nullptr,
295 r_ij
, r_kj
, r_kl
, m
, n
, &t1
, &t2
, &t3
);
296 dih
->param
[i
].c0() = ph
;
300 static void dump_hybridization(FILE *fp
, t_atoms
*atoms
, int nbonds
[])
304 for (i
= 0; (i
< atoms
->nr
); i
++)
306 fprintf(fp
, "Atom %5s has %1d bonds\n", *atoms
->atomname
[i
], nbonds
[i
]);
310 static void print_pl(FILE *fp
, t_params plist
[], int ftp
, const char *name
,
313 int i
, j
, nral
, nrfp
;
315 if (plist
[ftp
].nr
> 0)
318 fprintf(fp
, "[ %s ]\n", name
);
319 nral
= interaction_function
[ftp
].nratoms
;
320 nrfp
= interaction_function
[ftp
].nrfpA
;
321 for (i
= 0; (i
< plist
[ftp
].nr
); i
++)
323 for (j
= 0; (j
< nral
); j
++)
325 fprintf(fp
, " %5s", *atomname
[plist
[ftp
].param
[i
].a
[j
]]);
327 for (j
= 0; (j
< nrfp
); j
++)
329 if (plist
[ftp
].param
[i
].c
[j
] != NOTSET
)
331 fprintf(fp
, " %10.3e", plist
[ftp
].param
[i
].c
[j
]);
339 static void print_rtp(const char *filenm
, const char *title
, t_atoms
*atoms
,
340 t_params plist
[], gpp_atomtype
*atype
, int cgnr
[])
346 fp
= gmx_fio_fopen(filenm
, "w");
347 fprintf(fp
, "; %s\n", title
);
349 fprintf(fp
, "[ %s ]\n", *atoms
->resinfo
[0].name
);
351 fprintf(fp
, "[ atoms ]\n");
352 for (i
= 0; (i
< atoms
->nr
); i
++)
354 tp
= atoms
->atom
[i
].type
;
355 if ((tpnm
= get_atomtype_name(tp
, atype
)) == nullptr)
357 gmx_fatal(FARGS
, "tp = %d, i = %d in print_rtp", tp
, i
);
359 fprintf(fp
, "%-8s %12s %8.4f %5d\n",
360 *atoms
->atomname
[i
], tpnm
,
361 atoms
->atom
[i
].q
, cgnr
[i
]);
363 print_pl(fp
, plist
, F_BONDS
, "bonds", atoms
->atomname
);
364 print_pl(fp
, plist
, F_ANGLES
, "angles", atoms
->atomname
);
365 print_pl(fp
, plist
, F_PDIHS
, "dihedrals", atoms
->atomname
);
366 print_pl(fp
, plist
, F_IDIHS
, "impropers", atoms
->atomname
);
371 int gmx_x2top(int argc
, char *argv
[])
373 const char *desc
[] = {
374 "[THISMODULE] generates a primitive topology from a coordinate file.",
375 "The program assumes all hydrogens are present when defining",
376 "the hybridization from the atom name and the number of bonds.",
377 "The program can also make an [REF].rtp[ref] entry, which you can then add",
378 "to the [REF].rtp[ref] database.[PAR]",
379 "When [TT]-param[tt] is set, equilibrium distances and angles",
380 "and force constants will be printed in the topology for all",
381 "interactions. The equilibrium distances and angles are taken",
382 "from the input coordinates, the force constant are set with",
383 "command line options.",
384 "The force fields somewhat supported currently are:[PAR]",
385 "G53a5 GROMOS96 53a5 Forcefield (official distribution)[PAR]",
386 "oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)[PAR]",
387 "The corresponding data files can be found in the library directory",
388 "with name [TT]atomname2type.n2t[tt]. Check Chapter 5 of the manual for more",
389 "information about file formats. By default, the force field selection",
390 "is interactive, but you can use the [TT]-ff[tt] option to specify",
391 "one of the short names above on the command line instead. In that",
392 "case [THISMODULE] just looks for the corresponding file.[PAR]",
394 const char *bugs
[] = {
395 "The atom type selection is primitive. Virtually no chemical knowledge is used",
396 "Periodic boundary conditions screw up the bonding",
397 "No improper dihedrals are generated",
398 "The atoms to atomtype translation table is incomplete ([TT]atomname2type.n2t[tt] file in the data directory). Please extend it and send the results back to the GROMACS crew."
401 t_params plist
[F_NRE
];
408 char forcefield
[32], ffdir
[STRLEN
];
409 rvec
*x
; /* coordinates? */
411 int bts
[] = { 1, 1, 1, 2 };
412 matrix box
; /* box length matrix */
413 int natoms
; /* number of atoms in one molecule */
415 bool bRTP
, bTOP
, bOPLS
;
419 gmx_output_env_t
*oenv
;
422 { efSTX
, "-f", "conf", ffREAD
},
423 { efTOP
, "-o", "out", ffOPTWR
},
424 { efRTP
, "-r", "out", ffOPTWR
}
426 #define NFILE asize(fnm)
427 real kb
= 4e5
, kt
= 400, kp
= 5;
428 PreprocessResidue rtp_header_settings
;
429 bool bRemoveDihedralIfWithImproper
= FALSE
;
430 bool bGenerateHH14Interactions
= TRUE
;
431 bool bKeepAllGeneratedDihedrals
= FALSE
;
433 bool bParam
= TRUE
, bRound
= TRUE
;
434 bool bPairs
= TRUE
, bPBC
= TRUE
;
435 bool bUsePDBcharge
= FALSE
, bVerbose
= FALSE
;
436 const char *molnm
= "ICE";
437 const char *ff
= "oplsaa";
439 { "-ff", FALSE
, etSTR
, {&ff
},
440 "Force field for your simulation. Type \"select\" for interactive selection." },
441 { "-v", FALSE
, etBOOL
, {&bVerbose
},
442 "Generate verbose output in the top file." },
443 { "-nexcl", FALSE
, etINT
, {&nrexcl
},
444 "Number of exclusions" },
445 { "-H14", FALSE
, etBOOL
, {&bGenerateHH14Interactions
},
446 "Use 3rd neighbour interactions for hydrogen atoms" },
447 { "-alldih", FALSE
, etBOOL
, {&bKeepAllGeneratedDihedrals
},
448 "Generate all proper dihedrals" },
449 { "-remdih", FALSE
, etBOOL
, {&bRemoveDihedralIfWithImproper
},
450 "Remove dihedrals on the same bond as an improper" },
451 { "-pairs", FALSE
, etBOOL
, {&bPairs
},
452 "Output 1-4 interactions (pairs) in topology file" },
453 { "-name", FALSE
, etSTR
, {&molnm
},
454 "Name of your molecule" },
455 { "-pbc", FALSE
, etBOOL
, {&bPBC
},
456 "Use periodic boundary conditions." },
457 { "-pdbq", FALSE
, etBOOL
, {&bUsePDBcharge
},
458 "Use the B-factor supplied in a [REF].pdb[ref] file for the atomic charges" },
459 { "-param", FALSE
, etBOOL
, {&bParam
},
460 "Print parameters in the output" },
461 { "-round", FALSE
, etBOOL
, {&bRound
},
462 "Round off measured values" },
463 { "-kb", FALSE
, etREAL
, {&kb
},
464 "Bonded force constant (kJ/mol/nm^2)" },
465 { "-kt", FALSE
, etREAL
, {&kt
},
466 "Angle force constant (kJ/mol/rad^2)" },
467 { "-kp", FALSE
, etREAL
, {&kp
},
468 "Dihedral angle force constant (kJ/mol/rad^2)" }
471 if (!parse_common_args(&argc
, argv
, 0, NFILE
, fnm
, asize(pa
), pa
,
472 asize(desc
), desc
, asize(bugs
), bugs
, &oenv
))
476 bRTP
= opt2bSet("-r", NFILE
, fnm
);
477 bTOP
= opt2bSet("-o", NFILE
, fnm
);
478 /* C89 requirements mean that these struct members cannot be used in
479 * the declaration of pa. So some temporary variables are needed. */
480 rtp_header_settings
.bRemoveDihedralIfWithImproper
= bRemoveDihedralIfWithImproper
;
481 rtp_header_settings
.bGenerateHH14Interactions
= bGenerateHH14Interactions
;
482 rtp_header_settings
.bKeepAllGeneratedDihedrals
= bKeepAllGeneratedDihedrals
;
483 rtp_header_settings
.nrexcl
= nrexcl
;
487 gmx_fatal(FARGS
, "Specify at least one output file");
490 /* Force field selection, interactive or direct */
491 choose_ff(strcmp(ff
, "select") == 0 ? nullptr : ff
,
492 forcefield
, sizeof(forcefield
),
493 ffdir
, sizeof(ffdir
));
495 bOPLS
= (strcmp(forcefield
, "oplsaa") == 0);
498 mymol
.name
= gmx_strdup(molnm
);
501 /* Init parameter lists */
504 /* Read coordinates */
507 read_tps_conf(opt2fn("-f", NFILE
, fnm
), top
, &epbc
, &x
, nullptr, box
, FALSE
);
508 t_atoms
*atoms
= &top
->atoms
;
510 if (atoms
->pdbinfo
== nullptr)
512 snew(atoms
->pdbinfo
, natoms
);
515 sprintf(n2t
, "%s", ffdir
);
516 nm2t
= rd_nm2type(n2t
, &nnm
);
519 gmx_fatal(FARGS
, "No or incorrect atomname2type.n2t file found (looking for %s)",
524 printf("There are %d name to type translations in file %s\n", nnm
, n2t
);
528 dump_nm2type(debug
, nnm
, nm2t
);
530 printf("Generating bonds from distances...\n");
531 snew(nbonds
, atoms
->nr
);
532 mk_bonds(nnm
, nm2t
, atoms
, x
, &(plist
[F_BONDS
]), nbonds
, bPBC
, box
);
534 open_symtab(&symtab
);
535 atype
= set_atom_type(&symtab
, atoms
, &(plist
[F_BONDS
]), nbonds
, nnm
, nm2t
);
537 /* Make Angles and Dihedrals */
538 snew(excls
, atoms
->nr
);
539 printf("Generating angles and dihedrals from bonds...\n");
540 init_nnb(&nnb
, atoms
->nr
, 4);
541 gen_nnb(&nnb
, plist
);
542 print_nnb(&nnb
, "NNB");
543 gen_pad(&nnb
, atoms
, gmx::arrayRefFromArray(&rtp_header_settings
, 1), plist
, excls
, {}, TRUE
);
548 plist
[F_LJ14
].nr
= 0;
551 "There are %4d %s dihedrals, %4d impropers, %4d angles\n"
552 " %4d pairs, %4d bonds and %4d atoms\n",
554 bOPLS
? "Ryckaert-Bellemans" : "proper",
555 plist
[F_IDIHS
].nr
, plist
[F_ANGLES
].nr
,
556 plist
[F_LJ14
].nr
, plist
[F_BONDS
].nr
, atoms
->nr
);
558 calc_angles_dihs(&plist
[F_ANGLES
], &plist
[F_PDIHS
], x
, bPBC
, box
);
560 set_force_const(plist
, kb
, kt
, kp
, bRound
, bParam
);
562 cgnr
= set_cgnr(atoms
, bUsePDBcharge
, &qtot
, &mtot
);
563 printf("Total charge is %g, total mass is %g\n", qtot
, mtot
);
572 fp
= ftp2FILE(efTOP
, NFILE
, fnm
, "w");
573 print_top_header(fp
, ftp2fn(efTOP
, NFILE
, fnm
), TRUE
, ffdir
, 1.0);
575 write_top(fp
, nullptr, mymol
.name
.c_str(), atoms
, FALSE
, bts
, plist
, excls
, atype
,
576 cgnr
, rtp_header_settings
.nrexcl
);
577 print_top_mols(fp
, mymol
.name
.c_str(), ffdir
, nullptr, {}, gmx::arrayRefFromArray(&mymol
, 1));
583 print_rtp(ftp2fn(efRTP
, NFILE
, fnm
), "Generated by x2top",
584 atoms
, plist
, atype
, cgnr
);
589 dump_hybridization(debug
, atoms
, nbonds
);
591 close_symtab(&symtab
);
593 printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",
594 output_env_get_program_display_name(oenv
));
595 printf(" Please verify atomtypes and charges by comparison to other\n");
596 printf(" topologies.\n");