# HG changeset patch # User chemteam # Date 1643307425 0 # Node ID 9faa4f4b8b76860f290d6b3c8f889d105f9bc9d6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors commit ae026d4ea6fe2ebaa53611b86f9047941c7b899b" diff -r 000000000000 -r 9faa4f4b8b76 extract_top.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_top.xml Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,68 @@ + + from a GROMACS topology file + + + macros.xml + 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + doi:10.1186/1756-0500-5-367 + + diff -r 000000000000 -r 9faa4f4b8b76 gmxtras_add_newmolparam.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmxtras_add_newmolparam.py Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,45 @@ +#!/usr/bin/env python3 +import argparse + + +def __main__(): + parser = argparse.ArgumentParser( + description='Adds New topologies to gromacs topology file') + parser.add_argument( + '--top_file', default=None, + help="Topology file input") + parser.add_argument( + '--mol_file', default=None, + help='molecule type and bonded parameters input') + parser.add_argument( + '--atom_file', default=None, + help='atomtype and nonbonded parameters input') + parser.add_argument( + '--out', default=None, + help='Path to output') + args = parser.parse_args() + with open(args.out, 'w') as fh_out: + with open(args.top_file, 'r') as fh: + # these two short loop takes care of + # adding the atom types and molecule types. + for line in fh: + fh_out.write(line) + if ';name bond_type' in line: + for contents in open(args.atom_file): + fh_out.write(contents) + break + for line in fh: + if '[ system ]' in line: + fh_out.write("\n; Begin NewTopologyInfo\n") + for contents in open(args.mol_file): + fh_out.write(contents) + fh_out.write("; end NewTopologyInfo\n\n") + fh_out.write(line) + break + fh_out.write(line) + for line in fh: + fh_out.write(line) + + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 9faa4f4b8b76 gmxtras_add_restraints.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmxtras_add_restraints.py Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,71 @@ +#!/usr/bin/env python3 +import argparse +END_OF_MOL = ('[ moleculetype ]', '[ system ]') + + +def __main__(): + parser = argparse.ArgumentParser( + description='Add restriction to gromacs topology file') + parser.add_argument( + '--top_file', default=None, + help="Topology file input") + parser.add_argument( + '--res_file', default=None, + help='Restraint input') + parser.add_argument( + '--molecule', default=None, + help='Target Molecule Name you restrained') + parser.add_argument( + '--out', default=None, + help='Path to output') + args = parser.parse_args() + with open(args.out, 'w') as fh_out: + with open(args.top_file, 'r') as fh: + # for now, we will avoid using 'for line in fh:', + # since we have multiple places where we might want + # to read the next line + while True: + line = fh.readline() + if not line: + # eof + break + # always write out the line + fh_out.write(line) + # check if line matches molecule, then check if + # molecule name matches args.molecule + if line.strip().startswith('[ moleculetype ]'): + not_found_molecule = True + while not_found_molecule: + line = fh.readline() + if not line: + # eof + break + # always write this line + fh_out.write(line) + if not line.strip().startswith(';') or (line.strip() + and not line.strip().startswith(';')): + # this line should be the name line, + fields = line.strip().split() + if fields[0] == args.molecule: + # found our molecule! + while True: + line = fh.readline() + if not line: + # eof + break + if line.strip().startswith(END_OF_MOL): + fh_out.write("\n#ifdef POSRES\n") + with open(args.res_file, 'r') as fh_re: + for line2 in fh_re: + fh_out.write(line2) + fh_out.write("#endif\n\n") + fh_out.write(line) + not_found_molecule = False + break + fh_out.write(line) + else: + break + + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 9faa4f4b8b76 gmxtras_extract_top.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmxtras_extract_top.py Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,49 @@ +#!/usr/bin/env python3 +import argparse + + +def __main__(): + parser = argparse.ArgumentParser( + description='Adds New topologies to gromacs topology file') + parser.add_argument( + '--top_file', default=None, + help="Topologies input") + parser.add_argument( + '--out_bondparam', default=None, + help='moleculetype section') + parser.add_argument( + '--out_nonbondparam', default=None, + help='atomtypes section') + + args = parser.parse_args() + # extracts the atom types with nonbonded terms from + # the new molecules and puts them in a new file + with open(args.top_file) as inFile: + with open(args.out_nonbondparam, "w") as outFile: + buffer = [] + for line in inFile: + if line.startswith(";name bond_type"): + buffer = [''] + elif line.startswith("[ moleculetype ]"): + outFile.write("".join(buffer)) + buffer = [] + elif buffer: + buffer.append(line) + + # extracts the molecule types (rest of the force field parameters) + # with bonded terms and puts them in a new file + with open(args.top_file) as inFile: + with open(args.out_bondparam, "w") as outFile: + buffer = [] + for line in inFile: + if line.startswith("[ moleculetype ]"): + buffer = ["\n[ moleculetype ]\n"] + elif line.startswith("[ system ]"): + outFile.write("".join(buffer)) + buffer = [] + elif buffer: + buffer.append(line) + + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 9faa4f4b8b76 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,15 @@ + + 0 + + + python + + + + + + 10.1016/j.softx.2015.06.001 + + + + diff -r 000000000000 -r 9faa4f4b8b76 test-data/cid1_GMX.gro --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cid1_GMX.gro Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,45 @@ +UNL_GMX.gro created by acpype (v: 2021-02-05T22:15:50CET) on Wed Dec 15 14:23:59 2021 + 42 + 1 UNL C1 1 41.372 -2.389 7.399 + 1 UNL C2 2 41.301 -2.314 7.306 + 1 UNL C3 3 41.041 -2.283 7.776 + 1 UNL C4 4 41.308 -2.500 7.454 + 1 UNL C5 5 41.117 -2.462 7.333 + 1 UNL C6 6 41.214 -2.146 7.824 + 1 UNL C7 7 41.171 -2.350 7.272 + 1 UNL C8 8 41.136 -2.247 7.876 + 1 UNL C9 9 41.064 -2.202 7.667 + 1 UNL C10 10 40.992 -2.201 7.537 + 1 UNL C11 11 41.036 -2.061 7.071 + 1 UNL C12 12 41.128 -2.130 6.971 + 1 UNL C13 13 41.092 -2.270 7.171 + 1 UNL C14 14 41.077 -2.120 7.205 + 1 UNL C15 15 41.109 -2.380 6.943 + 1 UNL C16 16 40.975 -2.093 7.314 + 1 UNL N17 17 41.182 -2.538 7.424 + 1 UNL N18 18 41.169 -2.119 7.697 + 1 UNL N19 19 41.036 -2.108 7.442 + 1 UNL N20 20 41.154 -2.267 7.031 + 1 UNL O21 21 40.897 -2.277 7.520 + 1 UNL CL22 22 41.149 -2.318 8.029 + 1 UNL H23 23 41.473 -2.363 7.427 + 1 UNL H24 24 41.348 -2.227 7.261 + 1 UNL H25 25 40.965 -2.359 7.784 + 1 UNL H26 26 41.359 -2.562 7.527 + 1 UNL H27 27 41.016 -2.495 7.310 + 1 UNL H28 28 41.296 -2.090 7.865 + 1 UNL H29 29 41.046 -1.952 7.068 + 1 UNL H30 30 40.931 -2.085 7.048 + 1 UNL H31 31 41.084 -2.140 6.872 + 1 UNL H32 32 41.225 -2.080 6.965 + 1 UNL H33 33 40.992 -2.317 7.160 + 1 UNL H34 34 41.174 -2.078 7.235 + 1 UNL H35 35 41.000 -2.372 6.932 + 1 UNL H36 36 41.159 -2.370 6.847 + 1 UNL H37 37 41.136 -2.474 6.993 + 1 UNL H38 38 40.893 -2.164 7.305 + 1 UNL H39 39 40.938 -1.991 7.304 + 1 UNL H40 40 41.208 -2.049 7.635 + 1 UNL H41 41 41.111 -2.044 7.468 + 1 UNL H42 42 41.256 -2.276 7.041 + 11.59200 12.19000 23.64000 diff -r 000000000000 -r 9faa4f4b8b76 test-data/cid1_GMX.top --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cid1_GMX.top Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,476 @@ +; cid1_GMX.top created by acpype (v: 2021-02-05T22:15:50CET) on Wed Dec 15 14:23:59 2021 + +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ +1 2 yes 0.5 0.8333 + +[ atomtypes ] +;name bond_type mass charge ptype sigma epsilon Amb + ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + cc cc 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + cd cd 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 + c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 + nb nb 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + na na 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + n n 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + n4 n4 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 + o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 + cl cl 0.00000 0.00000 A 3.47094e-01 1.10876e+00 ; 1.95 0.2650 + ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 + h4 h4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 + hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 + hx hx 0.00000 0.00000 A 1.95998e-01 6.56888e-02 ; 1.10 0.0157 + h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 + hn hn 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 + +[ moleculetype ] +;name nrexcl + cid1 3 + +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 ca 1 cid1 C1 1 -0.236300 12.01000 ; qtot -0.236 + 2 ca 1 cid1 C2 2 -0.079000 12.01000 ; qtot -0.315 + 3 cc 1 cid1 C3 3 -0.068000 12.01000 ; qtot -0.383 + 4 ca 1 cid1 C4 4 0.441200 12.01000 ; qtot 0.058 + 5 ca 1 cid1 C5 5 0.436200 12.01000 ; qtot 0.494 + 6 cd 1 cid1 C6 6 -0.088300 12.01000 ; qtot 0.406 + 7 ca 1 cid1 C7 7 -0.300600 12.01000 ; qtot 0.105 + 8 cc 1 cid1 C8 8 -0.083600 12.01000 ; qtot 0.022 + 9 cd 1 cid1 C9 9 -0.229900 12.01000 ; qtot -0.208 + 10 c 1 cid1 C10 10 0.721699 12.01000 ; qtot 0.513 + 11 c3 1 cid1 C11 11 -0.099400 12.01000 ; qtot 0.414 + 12 c3 1 cid1 C12 12 0.108800 12.01000 ; qtot 0.523 + 13 c3 1 cid1 C13 13 0.196800 12.01000 ; qtot 0.720 + 14 c3 1 cid1 C14 14 -0.100700 12.01000 ; qtot 0.619 + 15 c3 1 cid1 C15 15 0.080100 12.01000 ; qtot 0.699 + 16 c3 1 cid1 C16 16 0.099000 12.01000 ; qtot 0.798 + 17 nb 1 cid1 N17 17 -0.641000 14.01000 ; qtot 0.157 + 18 na 1 cid1 N18 18 -0.155100 14.01000 ; qtot 0.002 + 19 n 1 cid1 N19 19 -0.586900 14.01000 ; qtot -0.585 + 20 n4 1 cid1 N20 20 -0.687400 14.01000 ; qtot -1.272 + 21 o 1 cid1 O21 21 -0.656100 16.00000 ; qtot -1.929 + 22 cl 1 cid1 CL22 22 -0.020400 35.45000 ; qtot -1.949 + 23 ha 1 cid1 H23 23 0.169000 1.00800 ; qtot -1.780 + 24 ha 1 cid1 H24 24 0.138000 1.00800 ; qtot -1.642 + 25 ha 1 cid1 H25 25 0.181000 1.00800 ; qtot -1.461 + 26 h4 1 cid1 H26 26 0.052100 1.00800 ; qtot -1.409 + 27 h4 1 cid1 H27 27 0.039100 1.00800 ; qtot -1.370 + 28 h4 1 cid1 H28 28 0.195000 1.00800 ; qtot -1.175 + 29 hc 1 cid1 H29 29 0.088700 1.00800 ; qtot -1.086 + 30 hc 1 cid1 H30 30 0.088700 1.00800 ; qtot -0.997 + 31 hx 1 cid1 H31 31 0.103700 1.00800 ; qtot -0.894 + 32 hx 1 cid1 H32 32 0.103700 1.00800 ; qtot -0.790 + 33 hx 1 cid1 H33 33 0.143700 1.00800 ; qtot -0.646 + 34 hc 1 cid1 H34 34 0.103700 1.00800 ; qtot -0.543 + 35 hx 1 cid1 H35 35 0.110367 1.00800 ; qtot -0.432 + 36 hx 1 cid1 H36 36 0.110367 1.00800 ; qtot -0.322 + 37 hx 1 cid1 H37 37 0.110367 1.00800 ; qtot -0.211 + 38 h1 1 cid1 H38 38 0.069700 1.00800 ; qtot -0.142 + 39 h1 1 cid1 H39 39 0.069700 1.00800 ; qtot -0.072 + 40 hn 1 cid1 H40 40 0.302700 1.00800 ; qtot 0.231 + 41 hn 1 cid1 H41 41 0.322500 1.00800 ; qtot 0.553 + 42 hn 1 cid1 H42 42 0.446800 1.00800 ; qtot 1.000 + +[ bonds ] +; ai aj funct r k + 1 2 1 1.3984e-01 3.8585e+05 ; C1 - C2 + 1 4 1 1.3984e-01 3.8585e+05 ; C1 - C4 + 1 23 1 1.0860e-01 2.8937e+05 ; C1 - H23 + 2 7 1 1.3984e-01 3.8585e+05 ; C2 - C7 + 2 24 1 1.0860e-01 2.8937e+05 ; C2 - H24 + 3 8 1 1.4278e-01 3.5129e+05 ; C3 - C8 + 3 9 1 1.3729e-01 4.1915e+05 ; C3 - C9 + 3 25 1 1.0837e-01 2.9213e+05 ; C3 - H25 + 4 17 1 1.3390e-01 4.0836e+05 ; C4 - N17 + 4 26 1 1.0890e-01 2.8577e+05 ; C4 - H26 + 5 7 1 1.3984e-01 3.8585e+05 ; C5 - C7 + 5 17 1 1.3390e-01 4.0836e+05 ; C5 - N17 + 5 27 1 1.0890e-01 2.8577e+05 ; C5 - H27 + 6 8 1 1.3729e-01 4.1915e+05 ; C6 - C8 + 6 18 1 1.3802e-01 3.5631e+05 ; C6 - N18 + 6 28 1 1.0817e-01 2.9455e+05 ; C6 - H28 + 7 13 1 1.5156e-01 2.6861e+05 ; C7 - C13 + 8 22 1 1.7354e-01 2.6568e+05 ; C8 - CL22 + 9 10 1 1.4676e-01 3.1045e+05 ; C9 - C10 + 9 18 1 1.3802e-01 3.5631e+05 ; C9 - N18 + 10 19 1 1.3789e-01 3.5782e+05 ; C10 - N19 + 10 21 1 1.2183e-01 5.3363e+05 ; C10 - O21 + 11 12 1 1.5375e-01 2.5179e+05 ; C11 - C12 + 11 14 1 1.5375e-01 2.5179e+05 ; C11 - C14 + 11 29 1 1.0969e-01 2.7665e+05 ; C11 - H29 + 11 30 1 1.0969e-01 2.7665e+05 ; C11 - H30 + 12 20 1 1.5110e-01 2.3707e+05 ; C12 - N20 + 12 31 1 1.0910e-01 2.8342e+05 ; C12 - H31 + 12 32 1 1.0910e-01 2.8342e+05 ; C12 - H32 + 13 14 1 1.5375e-01 2.5179e+05 ; C13 - C14 + 13 20 1 1.5110e-01 2.3707e+05 ; C13 - N20 + 13 33 1 1.0910e-01 2.8342e+05 ; C13 - H33 + 14 16 1 1.5375e-01 2.5179e+05 ; C14 - C16 + 14 34 1 1.0969e-01 2.7665e+05 ; C14 - H34 + 15 20 1 1.5110e-01 2.3707e+05 ; C15 - N20 + 15 35 1 1.0910e-01 2.8342e+05 ; C15 - H35 + 15 36 1 1.0910e-01 2.8342e+05 ; C15 - H36 + 15 37 1 1.0910e-01 2.8342e+05 ; C15 - H37 + 16 19 1 1.4619e-01 2.7506e+05 ; C16 - N19 + 16 38 1 1.0969e-01 2.7665e+05 ; C16 - H38 + 16 39 1 1.0969e-01 2.7665e+05 ; C16 - H39 + 18 40 1 1.0100e-01 3.4175e+05 ; N18 - H40 + 19 41 1 1.0129e-01 3.3740e+05 ; N19 - H41 + 20 42 1 1.0304e-01 3.1229e+05 ; N20 - H42 + +[ pairs ] +; ai aj funct + 1 5 1 ; C1 - C5 + 1 13 1 ; C1 - C13 + 2 14 1 ; C2 - C14 + 2 17 1 ; C2 - N17 + 2 20 1 ; C2 - N20 + 2 26 1 ; C2 - H26 + 2 27 1 ; C2 - H27 + 2 33 1 ; C2 - H33 + 3 19 1 ; C3 - N19 + 3 21 1 ; C3 - O21 + 3 28 1 ; C3 - H28 + 3 40 1 ; C3 - H40 + 4 7 1 ; C4 - C7 + 4 24 1 ; C4 - H24 + 4 27 1 ; C4 - H27 + 5 14 1 ; C5 - C14 + 5 20 1 ; C5 - N20 + 5 24 1 ; C5 - H24 + 5 26 1 ; C5 - H26 + 5 33 1 ; C5 - H33 + 6 10 1 ; C6 - C10 + 6 25 1 ; C6 - H25 + 7 11 1 ; C7 - C11 + 7 12 1 ; C7 - C12 + 7 15 1 ; C7 - C15 + 7 16 1 ; C7 - C16 + 7 34 1 ; C7 - H34 + 7 42 1 ; C7 - H42 + 8 10 1 ; C8 - C10 + 8 40 1 ; C8 - H40 + 9 16 1 ; C9 - C16 + 9 22 1 ; C9 - CL22 + 9 28 1 ; C9 - H28 + 9 41 1 ; C9 - H41 + 10 14 1 ; C10 - C14 + 10 25 1 ; C10 - H25 + 10 38 1 ; C10 - H38 + 10 39 1 ; C10 - H39 + 10 40 1 ; C10 - H40 + 11 15 1 ; C11 - C15 + 11 19 1 ; C11 - N19 + 11 33 1 ; C11 - H33 + 11 38 1 ; C11 - H38 + 11 39 1 ; C11 - H39 + 11 42 1 ; C11 - H42 + 12 16 1 ; C12 - C16 + 12 33 1 ; C12 - H33 + 12 34 1 ; C12 - H34 + 12 35 1 ; C12 - H35 + 12 36 1 ; C12 - H36 + 12 37 1 ; C12 - H37 + 13 17 1 ; C13 - N17 + 13 19 1 ; C13 - N19 + 13 24 1 ; C13 - H24 + 13 27 1 ; C13 - H27 + 13 29 1 ; C13 - H29 + 13 30 1 ; C13 - H30 + 13 31 1 ; C13 - H31 + 13 32 1 ; C13 - H32 + 13 35 1 ; C13 - H35 + 13 36 1 ; C13 - H36 + 13 37 1 ; C13 - H37 + 13 38 1 ; C13 - H38 + 13 39 1 ; C13 - H39 + 14 15 1 ; C14 - C15 + 14 31 1 ; C14 - H31 + 14 32 1 ; C14 - H32 + 14 41 1 ; C14 - H41 + 14 42 1 ; C14 - H42 + 15 31 1 ; C15 - H31 + 15 32 1 ; C15 - H32 + 15 33 1 ; C15 - H33 + 16 20 1 ; C16 - N20 + 16 21 1 ; C16 - O21 + 16 29 1 ; C16 - H29 + 16 30 1 ; C16 - H30 + 16 33 1 ; C16 - H33 + 18 19 1 ; N18 - N19 + 18 21 1 ; N18 - O21 + 18 22 1 ; N18 - CL22 + 18 25 1 ; N18 - H25 + 19 34 1 ; N19 - H34 + 20 29 1 ; N20 - H29 + 20 30 1 ; N20 - H30 + 20 34 1 ; N20 - H34 + 21 41 1 ; O21 - H41 + 22 25 1 ; CL22 - H25 + 22 28 1 ; CL22 - H28 + 23 7 1 ; H23 - C7 + 23 17 1 ; H23 - N17 + 23 24 1 ; H23 - H24 + 23 26 1 ; H23 - H26 + 28 40 1 ; H28 - H40 + 29 31 1 ; H29 - H31 + 29 32 1 ; H29 - H32 + 29 34 1 ; H29 - H34 + 30 31 1 ; H30 - H31 + 30 32 1 ; H30 - H32 + 30 34 1 ; H30 - H34 + 31 42 1 ; H31 - H42 + 32 42 1 ; H32 - H42 + 33 34 1 ; H33 - H34 + 33 42 1 ; H33 - H42 + 34 38 1 ; H34 - H38 + 34 39 1 ; H34 - H39 + 35 42 1 ; H35 - H42 + 36 42 1 ; H36 - H42 + 37 42 1 ; H37 - H42 + 38 41 1 ; H38 - H41 + 39 41 1 ; H39 - H41 + +[ angles ] +; ai aj ak funct theta cth + 1 2 7 1 1.2002e+02 5.5731e+02 ; C1 - C2 - C7 + 1 2 24 1 1.1988e+02 4.0334e+02 ; C1 - C2 - H24 + 1 4 17 1 1.2294e+02 5.7572e+02 ; C1 - C4 - N17 + 1 4 26 1 1.2034e+02 4.0250e+02 ; C1 - C4 - H26 + 2 1 4 1 1.2002e+02 5.5731e+02 ; C2 - C1 - C4 + 2 1 23 1 1.1988e+02 4.0334e+02 ; C2 - C1 - H23 + 2 7 5 1 1.2002e+02 5.5731e+02 ; C2 - C7 - C5 + 2 7 13 1 1.2077e+02 5.3137e+02 ; C2 - C7 - C13 + 3 8 6 1 1.1419e+02 5.7070e+02 ; C3 - C8 - C6 + 3 8 22 1 1.1999e+02 4.8367e+02 ; C3 - C8 - CL22 + 3 9 10 1 1.2135e+02 5.4476e+02 ; C3 - C9 - C10 + 3 9 18 1 1.0699e+02 6.1421e+02 ; C3 - C9 - N18 + 4 1 23 1 1.1988e+02 4.0334e+02 ; C4 - C1 - H23 + 4 17 5 1 1.1722e+02 5.7153e+02 ; C4 - N17 - C5 + 5 7 13 1 1.2077e+02 5.3137e+02 ; C5 - C7 - C13 + 6 8 22 1 1.2341e+02 4.8116e+02 ; C6 - C8 - CL22 + 6 18 9 1 1.0990e+02 5.7321e+02 ; C6 - N18 - C9 + 6 18 40 1 1.2550e+02 3.9162e+02 ; C6 - N18 - H40 + 7 2 24 1 1.1988e+02 4.0334e+02 ; C7 - C2 - H24 + 7 5 17 1 1.2294e+02 5.7572e+02 ; C7 - C5 - N17 + 7 5 27 1 1.2034e+02 4.0250e+02 ; C7 - C5 - H27 + 7 13 14 1 1.1207e+02 5.2802e+02 ; C7 - C13 - C14 + 7 13 20 1 1.1380e+02 5.4225e+02 ; C7 - C13 - N20 + 7 13 33 1 1.1145e+02 3.8995e+02 ; C7 - C13 - H33 + 8 3 9 1 1.1419e+02 5.7070e+02 ; C8 - C3 - C9 + 8 3 25 1 1.2107e+02 3.9413e+02 ; C8 - C3 - H25 + 8 6 18 1 1.0699e+02 6.1421e+02 ; C8 - C6 - N18 + 8 6 28 1 1.2848e+02 3.9581e+02 ; C8 - C6 - H28 + 9 3 25 1 1.2176e+02 4.0585e+02 ; C9 - C3 - H25 + 9 10 19 1 1.1270e+02 5.7823e+02 ; C9 - C10 - N19 + 9 10 21 1 1.2393e+02 5.7823e+02 ; C9 - C10 - O21 + 9 18 40 1 1.2550e+02 3.9162e+02 ; C9 - N18 - H40 + 10 9 18 1 1.1384e+02 5.7484e+02 ; C10 - C9 - N18 + 10 19 16 1 1.2069e+02 5.3053e+02 ; C10 - N19 - C16 + 10 19 41 1 1.1755e+02 4.0417e+02 ; C10 - N19 - H41 + 11 12 20 1 1.1421e+02 5.3723e+02 ; C11 - C12 - N20 + 11 12 31 1 1.1056e+02 3.8660e+02 ; C11 - C12 - H31 + 11 12 32 1 1.1056e+02 3.8660e+02 ; C11 - C12 - H32 + 11 14 13 1 1.1151e+02 5.2635e+02 ; C11 - C14 - C13 + 11 14 16 1 1.1151e+02 5.2635e+02 ; C11 - C14 - C16 + 11 14 34 1 1.0980e+02 3.8744e+02 ; C11 - C14 - H34 + 12 11 14 1 1.1151e+02 5.2635e+02 ; C12 - C11 - C14 + 12 11 29 1 1.0980e+02 3.8744e+02 ; C12 - C11 - H29 + 12 11 30 1 1.0980e+02 3.8744e+02 ; C12 - C11 - H30 + 12 20 13 1 1.0966e+02 5.2384e+02 ; C12 - N20 - C13 + 12 20 15 1 1.0966e+02 5.2384e+02 ; C12 - N20 - C15 + 12 20 42 1 1.1011e+02 3.8409e+02 ; C12 - N20 - H42 + 13 14 16 1 1.1151e+02 5.2635e+02 ; C13 - C14 - C16 + 13 14 34 1 1.0980e+02 3.8744e+02 ; C13 - C14 - H34 + 13 20 15 1 1.0966e+02 5.2384e+02 ; C13 - N20 - C15 + 13 20 42 1 1.1011e+02 3.8409e+02 ; C13 - N20 - H42 + 14 11 29 1 1.0980e+02 3.8744e+02 ; C14 - C11 - H29 + 14 11 30 1 1.0980e+02 3.8744e+02 ; C14 - C11 - H30 + 14 13 20 1 1.1421e+02 5.3723e+02 ; C14 - C13 - N20 + 14 13 33 1 1.1056e+02 3.8660e+02 ; C14 - C13 - H33 + 14 16 19 1 1.1161e+02 5.5145e+02 ; C14 - C16 - N19 + 14 16 38 1 1.0956e+02 3.8828e+02 ; C14 - C16 - H38 + 14 16 39 1 1.0956e+02 3.8828e+02 ; C14 - C16 - H39 + 15 20 42 1 1.1011e+02 3.8409e+02 ; C15 - N20 - H42 + 16 14 34 1 1.0980e+02 3.8744e+02 ; C16 - C14 - H34 + 16 19 41 1 1.1768e+02 3.8325e+02 ; C16 - N19 - H41 + 17 4 26 1 1.1603e+02 4.3430e+02 ; N17 - C4 - H26 + 17 5 27 1 1.1603e+02 4.3430e+02 ; N17 - C5 - H27 + 18 6 28 1 1.2053e+02 4.1673e+02 ; N18 - C6 - H28 + 19 10 21 1 1.2305e+02 6.2091e+02 ; N19 - C10 - O21 + 19 16 38 1 1.0888e+02 4.1673e+02 ; N19 - C16 - H38 + 19 16 39 1 1.0888e+02 4.1673e+02 ; N19 - C16 - H39 + 20 12 31 1 1.0801e+02 4.0668e+02 ; N20 - C12 - H31 + 20 12 32 1 1.0801e+02 4.0668e+02 ; N20 - C12 - H32 + 20 13 33 1 1.0801e+02 4.0668e+02 ; N20 - C13 - H33 + 20 15 35 1 1.0801e+02 4.0668e+02 ; N20 - C15 - H35 + 20 15 36 1 1.0801e+02 4.0668e+02 ; N20 - C15 - H36 + 20 15 37 1 1.0801e+02 4.0668e+02 ; N20 - C15 - H37 + 29 11 30 1 1.0758e+02 3.2970e+02 ; H29 - C11 - H30 + 31 12 32 1 1.0975e+02 3.2803e+02 ; H31 - C12 - H32 + 35 15 36 1 1.0975e+02 3.2803e+02 ; H35 - C15 - H36 + 35 15 37 1 1.0975e+02 3.2803e+02 ; H35 - C15 - H37 + 36 15 37 1 1.0975e+02 3.2803e+02 ; H36 - C15 - H37 + 38 16 39 1 1.0846e+02 3.2803e+02 ; H38 - C16 - H39 + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 2 7 5 9 180.00 15.16700 2 ; C1- C2- C7- C5 + 1 2 7 13 9 180.00 15.16700 2 ; C1- C2- C7- C13 + 1 4 17 5 9 180.00 20.08320 2 ; C1- C4- N17- C5 + 2 1 4 17 9 180.00 15.16700 2 ; C2- C1- C4- N17 + 2 1 4 26 9 180.00 15.16700 2 ; C2- C1- C4- H26 + 2 7 5 17 9 180.00 15.16700 2 ; C2- C7- C5- N17 + 2 7 5 27 9 180.00 15.16700 2 ; C2- C7- C5- H27 + 2 7 13 14 9 0.00 0.00000 0 ; C2- C7- C13- C14 + 2 7 13 20 9 0.00 0.00000 0 ; C2- C7- C13- N20 + 2 7 13 33 9 0.00 0.00000 0 ; C2- C7- C13- H33 + 3 8 6 18 9 180.00 16.73600 2 ; C3- C8- C6- N18 + 3 8 6 28 9 180.00 16.73600 2 ; C3- C8- C6- H28 + 3 9 10 19 9 180.00 12.02900 2 ; C3- C9- C10- N19 + 3 9 10 21 9 180.00 12.02900 2 ; C3- C9- C10- O21 + 3 9 18 6 9 180.00 7.11280 2 ; C3- C9- N18- C6 + 3 9 18 40 9 180.00 7.11280 2 ; C3- C9- N18- H40 + 4 1 2 7 9 180.00 15.16700 2 ; C4- C1- C2- C7 + 4 1 2 24 9 180.00 15.16700 2 ; C4- C1- C2- H24 + 4 17 5 7 9 180.00 20.08320 2 ; C4- N17- C5- C7 + 4 17 5 27 9 180.00 20.08320 2 ; C4- N17- C5- H27 + 5 7 2 24 9 180.00 15.16700 2 ; C5- C7- C2- H24 + 5 7 13 14 9 0.00 0.00000 0 ; C5- C7- C13- C14 + 5 7 13 20 9 0.00 0.00000 0 ; C5- C7- C13- N20 + 5 7 13 33 9 0.00 0.00000 0 ; C5- C7- C13- H33 + 5 17 4 26 9 180.00 20.08320 2 ; C5- N17- C4- H26 + 6 8 3 9 9 180.00 16.73600 2 ; C6- C8- C3- C9 + 6 8 3 25 9 180.00 16.73600 2 ; C6- C8- C3- H25 + 6 18 9 10 9 180.00 7.11280 2 ; C6- N18- C9- C10 + 7 13 14 11 9 0.00 0.65084 3 ; C7- C13- C14- C11 + 7 13 14 16 9 0.00 0.65084 3 ; C7- C13- C14- C16 + 7 13 14 34 9 0.00 0.65084 3 ; C7- C13- C14- H34 + 7 13 20 12 9 0.00 0.65084 3 ; C7- C13- N20- C12 + 7 13 20 12 9 0.00 2.92880 2 ; C7- C13- N20- C12 + 7 13 20 15 9 0.00 0.65084 3 ; C7- C13- N20- C15 + 7 13 20 15 9 0.00 2.92880 2 ; C7- C13- N20- C15 + 7 13 20 42 9 0.00 0.65084 3 ; C7- C13- N20- H42 + 8 3 9 10 9 180.00 16.73600 2 ; C8- C3- C9- C10 + 8 3 9 18 9 180.00 16.73600 2 ; C8- C3- C9- N18 + 8 6 18 9 9 180.00 7.11280 2 ; C8- C6- N18- C9 + 8 6 18 40 9 180.00 7.11280 2 ; C8- C6- N18- H40 + 9 3 8 22 9 180.00 16.73600 2 ; C9- C3- C8- CL22 + 9 10 19 16 9 180.00 10.46000 2 ; C9- C10- N19- C16 + 9 10 19 41 9 180.00 10.46000 2 ; C9- C10- N19- H41 + 9 18 6 28 9 180.00 7.11280 2 ; C9- N18- C6- H28 + 10 9 3 25 9 180.00 16.73600 2 ; C10- C9- C3- H25 + 10 9 18 40 9 180.00 7.11280 2 ; C10- C9- N18- H40 + 10 19 16 14 9 0.00 0.00000 0 ; C10- N19- C16- C14 + 10 19 16 14 9 0.00 2.21752 1 ; C10- N19- C16- C14 + 10 19 16 14 9 180.00 0.62760 3 ; C10- N19- C16- C14 + 10 19 16 14 9 180.00 2.09200 4 ; C10- N19- C16- C14 + 10 19 16 38 9 0.00 0.00000 0 ; C10- N19- C16- H38 + 10 19 16 39 9 0.00 0.00000 0 ; C10- N19- C16- H39 + 11 12 20 13 9 0.00 0.65084 3 ; C11- C12- N20- C13 + 11 12 20 15 9 0.00 0.65084 3 ; C11- C12- N20- C15 + 11 12 20 42 9 0.00 0.65084 3 ; C11- C12- N20- H42 + 11 14 13 20 9 0.00 0.65084 3 ; C11- C14- C13- N20 + 11 14 13 33 9 0.00 0.65084 3 ; C11- C14- C13- H33 + 11 14 16 19 9 0.00 0.65084 3 ; C11- C14- C16- N19 + 11 14 16 38 9 0.00 0.65084 3 ; C11- C14- C16- H38 + 11 14 16 39 9 0.00 0.65084 3 ; C11- C14- C16- H39 + 12 11 14 13 9 0.00 0.75312 3 ; C12- C11- C14- C13 + 12 11 14 13 9 180.00 0.83680 1 ; C12- C11- C14- C13 + 12 11 14 13 9 180.00 1.04600 2 ; C12- C11- C14- C13 + 12 11 14 16 9 0.00 0.75312 3 ; C12- C11- C14- C16 + 12 11 14 16 9 180.00 0.83680 1 ; C12- C11- C14- C16 + 12 11 14 16 9 180.00 1.04600 2 ; C12- C11- C14- C16 + 12 11 14 34 9 0.00 0.66944 3 ; C12- C11- C14- H34 + 12 20 13 14 9 0.00 0.65084 3 ; C12- N20- C13- C14 + 12 20 13 33 9 0.00 0.65084 3 ; C12- N20- C13- H33 + 12 20 15 35 9 0.00 0.65084 3 ; C12- N20- C15- H35 + 12 20 15 36 9 0.00 0.65084 3 ; C12- N20- C15- H36 + 12 20 15 37 9 0.00 0.65084 3 ; C12- N20- C15- H37 + 13 7 2 24 9 180.00 15.16700 2 ; C13- C7- C2- H24 + 13 7 5 17 9 180.00 15.16700 2 ; C13- C7- C5- N17 + 13 7 5 27 9 180.00 15.16700 2 ; C13- C7- C5- H27 + 13 14 11 29 9 0.00 0.66944 3 ; C13- C14- C11- H29 + 13 14 11 30 9 0.00 0.66944 3 ; C13- C14- C11- H30 + 13 14 16 19 9 0.00 0.65084 3 ; C13- C14- C16- N19 + 13 14 16 38 9 0.00 0.65084 3 ; C13- C14- C16- H38 + 13 14 16 39 9 0.00 0.65084 3 ; C13- C14- C16- H39 + 13 20 12 31 9 0.00 0.65084 3 ; C13- N20- C12- H31 + 13 20 12 32 9 0.00 0.65084 3 ; C13- N20- C12- H32 + 13 20 15 35 9 0.00 0.65084 3 ; C13- N20- C15- H35 + 13 20 15 36 9 0.00 0.65084 3 ; C13- N20- C15- H36 + 13 20 15 37 9 0.00 0.65084 3 ; C13- N20- C15- H37 + 14 11 12 20 9 0.00 0.65084 3 ; C14- C11- C12- N20 + 14 11 12 31 9 0.00 0.65084 3 ; C14- C11- C12- H31 + 14 11 12 32 9 0.00 0.65084 3 ; C14- C11- C12- H32 + 14 13 20 15 9 0.00 0.65084 3 ; C14- C13- N20- C15 + 14 13 20 42 9 0.00 0.65084 3 ; C14- C13- N20- H42 + 14 16 19 41 9 0.00 0.00000 0 ; C14- C16- N19- H41 + 15 20 12 31 9 0.00 0.65084 3 ; C15- N20- C12- H31 + 15 20 12 32 9 0.00 0.65084 3 ; C15- N20- C12- H32 + 15 20 13 33 9 0.00 0.65084 3 ; C15- N20- C13- H33 + 16 14 11 29 9 0.00 0.66944 3 ; C16- C14- C11- H29 + 16 14 11 30 9 0.00 0.66944 3 ; C16- C14- C11- H30 + 16 14 13 20 9 0.00 0.65084 3 ; C16- C14- C13- N20 + 16 14 13 33 9 0.00 0.65084 3 ; C16- C14- C13- H33 + 16 19 10 21 9 180.00 10.46000 2 ; C16- N19- C10- O21 + 18 6 8 22 9 180.00 16.73600 2 ; N18- C6- C8- CL22 + 18 9 3 25 9 180.00 16.73600 2 ; N18- C9- C3- H25 + 18 9 10 19 9 180.00 12.02900 2 ; N18- C9- C10- N19 + 18 9 10 21 9 180.00 12.02900 2 ; N18- C9- C10- O21 + 19 16 14 34 9 0.00 0.65084 3 ; N19- C16- C14- H34 + 20 12 11 29 9 0.00 0.65084 3 ; N20- C12- C11- H29 + 20 12 11 30 9 0.00 0.65084 3 ; N20- C12- C11- H30 + 20 13 14 34 9 0.00 0.65084 3 ; N20- C13- C14- H34 + 21 10 19 41 9 0.00 8.36800 1 ; O21- C10- N19- H41 + 21 10 19 41 9 180.00 10.46000 2 ; O21- C10- N19- H41 + 22 8 3 25 9 180.00 16.73600 2 ; CL22- C8- C3- H25 + 22 8 6 28 9 180.00 16.73600 2 ; CL22- C8- C6- H28 + 23 1 2 7 9 180.00 15.16700 2 ; H23- C1- C2- C7 + 23 1 2 24 9 180.00 15.16700 2 ; H23- C1- C2- H24 + 23 1 4 17 9 180.00 15.16700 2 ; H23- C1- C4- N17 + 23 1 4 26 9 180.00 15.16700 2 ; H23- C1- C4- H26 + 28 6 18 40 9 180.00 7.11280 2 ; H28- C6- N18- H40 + 29 11 12 31 9 0.00 0.65084 3 ; H29- C11- C12- H31 + 29 11 12 32 9 0.00 0.65084 3 ; H29- C11- C12- H32 + 29 11 14 34 9 0.00 0.62760 3 ; H29- C11- C14- H34 + 30 11 12 31 9 0.00 0.65084 3 ; H30- C11- C12- H31 + 30 11 12 32 9 0.00 0.65084 3 ; H30- C11- C12- H32 + 30 11 14 34 9 0.00 0.62760 3 ; H30- C11- C14- H34 + 31 12 20 42 9 0.00 0.65084 3 ; H31- C12- N20- H42 + 32 12 20 42 9 0.00 0.65084 3 ; H32- C12- N20- H42 + 33 13 14 34 9 0.00 0.65084 3 ; H33- C13- C14- H34 + 33 13 20 42 9 0.00 0.65084 3 ; H33- C13- N20- H42 + 34 14 16 38 9 0.00 0.65084 3 ; H34- C14- C16- H38 + 34 14 16 39 9 0.00 0.65084 3 ; H34- C14- C16- H39 + 35 15 20 42 9 0.00 0.65084 3 ; H35- C15- N20- H42 + 36 15 20 42 9 0.00 0.65084 3 ; H36- C15- N20- H42 + 37 15 20 42 9 0.00 0.65084 3 ; H37- C15- N20- H42 + 38 16 19 41 9 0.00 0.00000 0 ; H38- C16- N19- H41 + 39 16 19 41 9 0.00 0.00000 0 ; H39- C16- N19- H41 + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 1 7 2 24 4 180.00 4.60240 2 ; C1- C7- C2- H24 + 1 26 4 17 4 180.00 4.60240 2 ; C1- H26- C4- N17 + 2 5 7 13 4 180.00 4.60240 2 ; C2- C5- C7- C13 + 3 6 8 22 4 180.00 4.60240 2 ; C3- C6- C8- CL22 + 6 9 18 40 4 180.00 4.60240 2 ; C6- C9- N18- H40 + 7 27 5 17 4 180.00 4.60240 2 ; C7- H27- C5- N17 + 8 9 3 25 4 180.00 4.60240 2 ; C8- C9- C3- H25 + 8 28 6 18 4 180.00 4.60240 2 ; C8- H28- C6- N18 + 9 19 10 21 4 180.00 43.93200 2 ; C9- N19- C10- O21 + 10 3 9 18 4 180.00 4.60240 2 ; C10- C3- C9- N18 + 10 16 19 41 4 180.00 4.60240 2 ; C10- C16- N19- H41 + 23 1 4 2 4 180.00 4.60240 2 ; H23- C1- C4- C2 + +[ system ] + cid1 + +[ molecules ] +; Compound nmols + cid1 1 diff -r 000000000000 -r 9faa4f4b8b76 test-data/posres_cid1.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posres_cid1.itp Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,45 @@ + +[ position_restraints ] +; i funct fcx fcy fcz + 1 1 1000 1000 1000 + 2 1 1000 1000 1000 + 3 1 1000 1000 1000 + 4 1 1000 1000 1000 + 5 1 1000 1000 1000 + 6 1 1000 1000 1000 + 7 1 1000 1000 1000 + 8 1 1000 1000 1000 + 9 1 1000 1000 1000 + 10 1 1000 1000 1000 + 11 1 1000 1000 1000 + 12 1 1000 1000 1000 + 13 1 1000 1000 1000 + 14 1 1000 1000 1000 + 15 1 1000 1000 1000 + 16 1 1000 1000 1000 + 17 1 1000 1000 1000 + 18 1 1000 1000 1000 + 19 1 1000 1000 1000 + 20 1 1000 1000 1000 + 21 1 1000 1000 1000 + 22 1 1000 1000 1000 + 23 1 1000 1000 1000 + 24 1 1000 1000 1000 + 25 1 1000 1000 1000 + 26 1 1000 1000 1000 + 27 1 1000 1000 1000 + 28 1 1000 1000 1000 + 29 1 1000 1000 1000 + 30 1 1000 1000 1000 + 31 1 1000 1000 1000 + 32 1 1000 1000 1000 + 33 1 1000 1000 1000 + 34 1 1000 1000 1000 + 35 1 1000 1000 1000 + 36 1 1000 1000 1000 + 37 1 1000 1000 1000 + 38 1 1000 1000 1000 + 39 1 1000 1000 1000 + 40 1 1000 1000 1000 + 41 1 1000 1000 1000 + 42 1 1000 1000 1000 diff -r 000000000000 -r 9faa4f4b8b76 test-data/water_bondedparams.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/water_bondedparams.itp Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,61 @@ +; +; Horn et al. (2004). J. Chem. Phys.120, 9665-9678 +; + + +[ moleculetype ] +; molname nrexcl +SOL 2 + +[ atoms ] +; id at type res nr res name at name cg nr charge mass + 1 OW_tip4pew 1 SOL OW 1 0 16.00000 + 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 + 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 + 4 MW 1 SOL MW 1 -1.04844 0.00000 + +#ifndef FLEXIBLE + +[ settles ] +; i funct doh dhh +1 1 0.09572 0.15139 + +#else +[ bonds ] +; i j funct length force.c. +1 2 1 0.09572 502416.0 0.09572 502416.0 +1 3 1 0.09572 502416.0 0.09572 502416.0 + +[ angles ] +; i j k funct angle force.c. +2 1 3 1 104.52 628.02 104.52 628.02 + +#endif + + +[ virtual_sites3 ] +; Vsite from funct a b +4 1 2 3 1 0.106676721 0.106676721 + + +[ exclusions ] +1 2 3 4 +2 1 3 4 +3 1 2 4 +4 1 2 3 + + +; The position of the virtual site is computed as follows: +; +; O +; +; V +; +; H H +; +; Ewald tip4p: +; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] +; 0.0125 nm / [ cos (52.26 deg) * 0.09572 nm ] +; then a = b = 0.5 * const = 0.106676721 +; +; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) diff -r 000000000000 -r 9faa4f4b8b76 test-data/water_nonbondedparams.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/water_nonbondedparams.itp Thu Jan 27 18:17:05 2022 +0000 @@ -0,0 +1,3 @@ +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +MW 0 0.0000 0.0000 D 0.00000e+00 0.00000e+00