Mercurial > repos > chemteam > gmx_em
view test-data/topol_md.top @ 16:bfca1eee5aa2 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0"
| author | chemteam |
|---|---|
| date | Tue, 30 Nov 2021 15:28:31 +0000 |
| parents | d532b7e5f64b |
| children |
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; ; File 'topol.top' was generated ; By user: unknown (1000) ; On host: simon-notebook ; At date: Tue May 12 12:59:21 2020 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2019.1 (-: ; ; Executable: /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx ; Data prefix: /home/simon/miniconda3/envs/__gromacs@2019.1 ; Working dir: /tmp/tmpg0ncnt9q/job_working_directory/000/10/working ; Command line: ; gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all ; Force field was read from the standard GROMACS share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 LYS rtp LYSH q +2.0 1 opls_287 1 LYS N 1 -0.3 14.0027 2 opls_290 1 LYS H1 1 0.33 1.008 3 opls_290 1 LYS H2 1 0.33 1.008 4 opls_290 1 LYS H3 1 0.33 1.008 5 opls_293B 1 LYS CA 1 0.25 12.011 6 opls_140 1 LYS HA 1 0.06 1.008 7 opls_136 1 LYS CB 2 -0.12 12.011 8 opls_140 1 LYS HB1 2 0.06 1.008 9 opls_140 1 LYS HB2 2 0.06 1.008 10 opls_136 1 LYS CG 3 -0.12 12.011 11 opls_140 1 LYS HG1 3 0.06 1.008 12 opls_140 1 LYS HG2 3 0.06 1.008 13 opls_136 1 LYS CD 4 -0.12 12.011 14 opls_140 1 LYS HD1 4 0.06 1.008 15 opls_140 1 LYS HD2 4 0.06 1.008 16 opls_292 1 LYS CE 5 0.19 12.011 17 opls_140 1 LYS HE1 5 0.06 1.008 18 opls_140 1 LYS HE2 5 0.06 1.008 19 opls_287 1 LYS NZ 6 -0.3 14.0067 20 opls_290 1 LYS HZ1 6 0.33 1.008 21 opls_290 1 LYS HZ2 6 0.33 1.008 22 opls_290 1 LYS HZ3 6 0.33 1.008 23 opls_235 1 LYS C 7 0.5 12.011 24 opls_236 1 LYS O 7 -0.5 15.9994 ; qtot 2 ; residue 2 VAL rtp VAL q 0.0 25 opls_238 2 VAL N 8 -0.5 14.0067 26 opls_241 2 VAL H 8 0.3 1.008 27 opls_224B 2 VAL CA 8 0.14 12.011 28 opls_140 2 VAL HA 8 0.06 1.008 29 opls_137 2 VAL CB 9 -0.06 12.011 30 opls_140 2 VAL HB 9 0.06 1.008 31 opls_135 2 VAL CG1 10 -0.18 12.011 32 opls_140 2 VAL HG11 10 0.06 1.008 33 opls_140 2 VAL HG12 10 0.06 1.008 34 opls_140 2 VAL HG13 10 0.06 1.008 35 opls_135 2 VAL CG2 11 -0.18 12.011 36 opls_140 2 VAL HG21 11 0.06 1.008 37 opls_140 2 VAL HG22 11 0.06 1.008 38 opls_140 2 VAL HG23 11 0.06 1.008 39 opls_235 2 VAL C 12 0.5 12.011 40 opls_236 2 VAL O 12 -0.5 15.9994 ; qtot 2 ; residue 3 PHE rtp PHE q 0.0 41 opls_238 3 PHE N 13 -0.5 14.0067 42 opls_241 3 PHE H 13 0.3 1.008 43 opls_224B 3 PHE CA 13 0.14 12.011 44 opls_140 3 PHE HA 13 0.06 1.008 45 opls_149 3 PHE CB 14 -0.005 12.011 46 opls_140 3 PHE HB1 14 0.06 1.008 47 opls_140 3 PHE HB2 14 0.06 1.008 48 opls_145 3 PHE CG 14 -0.115 12.011 49 opls_145 3 PHE CD1 15 -0.115 12.011 50 opls_146 3 PHE HD1 15 0.115 1.008 51 opls_145 3 PHE CD2 16 -0.115 12.011 52 opls_146 3 PHE HD2 16 0.115 1.008 53 opls_145 3 PHE CE1 17 -0.115 12.011 54 opls_146 3 PHE HE1 17 0.115 1.008 55 opls_145 3 PHE CE2 18 -0.115 12.011 56 opls_146 3 PHE HE2 18 0.115 1.008 57 opls_145 3 PHE CZ 19 -0.115 12.011 58 opls_146 3 PHE HZ 19 0.115 1.008 59 opls_235 3 PHE C 20 0.5 12.011 60 opls_236 3 PHE O 20 -0.5 15.9994 ; qtot 2 ; residue 4 GLY rtp GLY q 0.0 61 opls_238 4 GLY N 21 -0.5 14.0067 62 opls_241 4 GLY H 21 0.3 1.008 63 opls_223B 4 GLY CA 21 0.08 12.011 64 opls_140 4 GLY HA1 21 0.06 1.008 65 opls_140 4 GLY HA2 21 0.06 1.008 66 opls_235 4 GLY C 22 0.5 12.011 67 opls_236 4 GLY O 22 -0.5 15.9994 ; qtot 2 ; residue 5 ARG rtp ARG q 0.0 68 opls_238 5 ARG N 23 -0.5 14.0067 69 opls_241 5 ARG H 23 0.3 1.008 70 opls_283 5 ARG CA 23 0.04 12.011 71 opls_140 5 ARG HA 23 0.06 1.008 72 opls_136 5 ARG CB 24 -0.12 12.011 73 opls_140 5 ARG HB1 24 0.06 1.008 74 opls_140 5 ARG HB2 24 0.06 1.008 75 opls_308 5 ARG CG 25 -0.05 12.011 76 opls_140 5 ARG HG1 25 0.06 1.008 77 opls_140 5 ARG HG2 25 0.06 1.008 78 opls_307 5 ARG CD 26 0.19 12.011 79 opls_140 5 ARG HD1 26 0.06 1.008 80 opls_140 5 ARG HD2 26 0.06 1.008 81 opls_303 5 ARG NE 27 -0.7 14.0067 82 opls_304 5 ARG HE 27 0.44 1.008 83 opls_302 5 ARG CZ 27 0.64 12.011 84 opls_300 5 ARG NH1 28 -0.8 14.0067 85 opls_301 5 ARG HH11 28 0.46 1.008 86 opls_301 5 ARG HH12 28 0.46 1.008 87 opls_300 5 ARG NH2 29 -0.8 14.0067 88 opls_301 5 ARG HH21 29 0.46 1.008 89 opls_301 5 ARG HH22 29 0.46 1.008 90 opls_271 5 ARG C 30 0.7 12.011 91 opls_272 5 ARG O1 30 -0.8 15.9994 92 opls_272 5 ARG O2 30 -0.8 15.9994 ; qtot 2 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 23 1 7 8 1 7 9 1 7 10 1 10 11 1 10 12 1 10 13 1 13 14 1 13 15 1 13 16 1 16 17 1 16 18 1 16 19 1 19 20 1 19 21 1 19 22 1 23 24 1 23 25 1 25 26 1 25 27 1 27 28 1 27 29 1 27 39 1 29 30 1 29 31 1 29 35 1 31 32 1 31 33 1 31 34 1 35 36 1 35 37 1 35 38 1 39 40 1 39 41 1 41 42 1 41 43 1 43 44 1 43 45 1 43 59 1 45 46 1 45 47 1 45 48 1 48 49 1 48 51 1 49 50 1 49 53 1 51 52 1 51 55 1 53 54 1 53 57 1 55 56 1 55 57 1 57 58 1 59 60 1 59 61 1 61 62 1 61 63 1 63 64 1 63 65 1 63 66 1 66 67 1 66 68 1 68 69 1 68 70 1 70 71 1 70 72 1 70 90 1 72 73 1 72 74 1 72 75 1 75 76 1 75 77 1 75 78 1 78 79 1 78 80 1 78 81 1 81 82 1 81 83 1 83 84 1 83 87 1 84 85 1 84 86 1 87 88 1 87 89 1 90 91 1 90 92 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 8 1 1 9 1 1 10 1 1 24 1 1 25 1 2 6 1 2 7 1 2 23 1 3 6 1 3 7 1 3 23 1 4 6 1 4 7 1 4 23 1 5 11 1 5 12 1 5 13 1 5 26 1 5 27 1 6 8 1 6 9 1 6 10 1 6 24 1 6 25 1 7 14 1 7 15 1 7 16 1 7 24 1 7 25 1 8 11 1 8 12 1 8 13 1 8 23 1 9 11 1 9 12 1 9 13 1 9 23 1 10 17 1 10 18 1 10 19 1 10 23 1 11 14 1 11 15 1 11 16 1 12 14 1 12 15 1 12 16 1 13 20 1 13 21 1 13 22 1 14 17 1 14 18 1 14 19 1 15 17 1 15 18 1 15 19 1 17 20 1 17 21 1 17 22 1 18 20 1 18 21 1 18 22 1 23 28 1 23 29 1 23 39 1 24 26 1 24 27 1 25 30 1 25 31 1 25 35 1 25 40 1 25 41 1 26 28 1 26 29 1 26 39 1 27 32 1 27 33 1 27 34 1 27 36 1 27 37 1 27 38 1 27 42 1 27 43 1 28 30 1 28 31 1 28 35 1 28 40 1 28 41 1 29 40 1 29 41 1 30 32 1 30 33 1 30 34 1 30 36 1 30 37 1 30 38 1 30 39 1 31 36 1 31 37 1 31 38 1 31 39 1 32 35 1 33 35 1 34 35 1 35 39 1 39 44 1 39 45 1 39 59 1 40 42 1 40 43 1 41 46 1 41 47 1 41 48 1 41 60 1 41 61 1 42 44 1 42 45 1 42 59 1 43 49 1 43 51 1 43 62 1 43 63 1 44 46 1 44 47 1 44 48 1 44 60 1 44 61 1 45 50 1 45 52 1 45 53 1 45 55 1 45 60 1 45 61 1 46 49 1 46 51 1 46 59 1 47 49 1 47 51 1 47 59 1 48 54 1 48 56 1 48 57 1 48 59 1 49 52 1 49 55 1 49 58 1 50 51 1 50 54 1 50 57 1 51 53 1 51 58 1 52 56 1 52 57 1 53 56 1 54 55 1 54 58 1 56 58 1 59 64 1 59 65 1 59 66 1 60 62 1 60 63 1 61 67 1 61 68 1 62 64 1 62 65 1 62 66 1 63 69 1 63 70 1 64 67 1 64 68 1 65 67 1 65 68 1 66 71 1 66 72 1 66 90 1 67 69 1 67 70 1 68 73 1 68 74 1 68 75 1 68 91 1 68 92 1 69 71 1 69 72 1 69 90 1 70 76 1 70 77 1 70 78 1 71 73 1 71 74 1 71 75 1 71 91 1 71 92 1 72 79 1 72 80 1 72 81 1 72 91 1 72 92 1 73 76 1 73 77 1 73 78 1 73 90 1 74 76 1 74 77 1 74 78 1 74 90 1 75 82 1 75 83 1 75 90 1 76 79 1 76 80 1 76 81 1 77 79 1 77 80 1 77 81 1 78 84 1 78 87 1 79 82 1 79 83 1 80 82 1 80 83 1 81 85 1 81 86 1 81 88 1 81 89 1 82 84 1 82 87 1 84 88 1 84 89 1 85 87 1 86 87 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 1 5 6 1 1 5 7 1 1 5 23 1 6 5 7 1 6 5 23 1 7 5 23 1 5 7 8 1 5 7 9 1 5 7 10 1 8 7 9 1 8 7 10 1 9 7 10 1 7 10 11 1 7 10 12 1 7 10 13 1 11 10 12 1 11 10 13 1 12 10 13 1 10 13 14 1 10 13 15 1 10 13 16 1 14 13 15 1 14 13 16 1 15 13 16 1 13 16 17 1 13 16 18 1 13 16 19 1 17 16 18 1 17 16 19 1 18 16 19 1 16 19 20 1 16 19 21 1 16 19 22 1 20 19 21 1 20 19 22 1 21 19 22 1 5 23 24 1 5 23 25 1 24 23 25 1 23 25 26 1 23 25 27 1 26 25 27 1 25 27 28 1 25 27 29 1 25 27 39 1 28 27 29 1 28 27 39 1 29 27 39 1 27 29 30 1 27 29 31 1 27 29 35 1 30 29 31 1 30 29 35 1 31 29 35 1 29 31 32 1 29 31 33 1 29 31 34 1 32 31 33 1 32 31 34 1 33 31 34 1 29 35 36 1 29 35 37 1 29 35 38 1 36 35 37 1 36 35 38 1 37 35 38 1 27 39 40 1 27 39 41 1 40 39 41 1 39 41 42 1 39 41 43 1 42 41 43 1 41 43 44 1 41 43 45 1 41 43 59 1 44 43 45 1 44 43 59 1 45 43 59 1 43 45 46 1 43 45 47 1 43 45 48 1 46 45 47 1 46 45 48 1 47 45 48 1 45 48 49 1 45 48 51 1 49 48 51 1 48 49 50 1 48 49 53 1 50 49 53 1 48 51 52 1 48 51 55 1 52 51 55 1 49 53 54 1 49 53 57 1 54 53 57 1 51 55 56 1 51 55 57 1 56 55 57 1 53 57 55 1 53 57 58 1 55 57 58 1 43 59 60 1 43 59 61 1 60 59 61 1 59 61 62 1 59 61 63 1 62 61 63 1 61 63 64 1 61 63 65 1 61 63 66 1 64 63 65 1 64 63 66 1 65 63 66 1 63 66 67 1 63 66 68 1 67 66 68 1 66 68 69 1 66 68 70 1 69 68 70 1 68 70 71 1 68 70 72 1 68 70 90 1 71 70 72 1 71 70 90 1 72 70 90 1 70 72 73 1 70 72 74 1 70 72 75 1 73 72 74 1 73 72 75 1 74 72 75 1 72 75 76 1 72 75 77 1 72 75 78 1 76 75 77 1 76 75 78 1 77 75 78 1 75 78 79 1 75 78 80 1 75 78 81 1 79 78 80 1 79 78 81 1 80 78 81 1 78 81 82 1 78 81 83 1 82 81 83 1 81 83 84 1 81 83 87 1 84 83 87 1 83 84 85 1 83 84 86 1 85 84 86 1 83 87 88 1 83 87 89 1 88 87 89 1 70 90 91 1 70 90 92 1 91 90 92 1 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 6 3 2 1 5 7 3 2 1 5 23 3 3 1 5 6 3 3 1 5 7 3 3 1 5 23 3 4 1 5 6 3 4 1 5 7 3 4 1 5 23 3 1 5 7 10 3 dih_LYS_chi1_N_C_C_C 23 5 7 10 3 dih_LYS_chi1_C_C_C_CO 1 5 7 8 3 1 5 7 9 3 6 5 7 8 3 6 5 7 9 3 6 5 7 10 3 23 5 7 8 3 23 5 7 9 3 1 5 23 24 3 1 5 23 25 3 6 5 23 24 3 6 5 23 25 3 7 5 23 24 3 7 5 23 25 3 5 7 10 11 3 5 7 10 12 3 5 7 10 13 3 8 7 10 11 3 8 7 10 12 3 8 7 10 13 3 9 7 10 11 3 9 7 10 12 3 9 7 10 13 3 7 10 13 14 3 7 10 13 15 3 7 10 13 16 3 11 10 13 14 3 11 10 13 15 3 11 10 13 16 3 12 10 13 14 3 12 10 13 15 3 12 10 13 16 3 10 13 16 17 3 10 13 16 18 3 10 13 16 19 3 14 13 16 17 3 14 13 16 18 3 14 13 16 19 3 15 13 16 17 3 15 13 16 18 3 15 13 16 19 3 13 16 19 20 3 dih_LYS_chi5_C_C_N_H 13 16 19 21 3 dih_LYS_chi5_C_C_N_H 13 16 19 22 3 dih_LYS_chi5_C_C_N_H 17 16 19 20 3 17 16 19 21 3 17 16 19 22 3 18 16 19 20 3 18 16 19 21 3 18 16 19 22 3 5 23 25 26 3 5 23 25 27 3 24 23 25 26 3 24 23 25 27 3 23 25 27 28 3 23 25 27 29 3 23 25 27 39 3 26 25 27 28 3 26 25 27 29 3 26 25 27 39 3 25 27 29 31 3 dih_VAL_chi1_N_C_C_C 25 27 29 35 3 dih_VAL_chi1_N_C_C_C 39 27 29 31 3 dih_VAL_chi1_C_C_C_CO 39 27 29 35 3 dih_VAL_chi1_C_C_C_CO 25 27 29 30 3 28 27 29 30 3 28 27 29 31 3 28 27 29 35 3 39 27 29 30 3 25 27 39 40 3 25 27 39 41 3 28 27 39 40 3 28 27 39 41 3 29 27 39 40 3 29 27 39 41 3 27 29 31 32 3 27 29 31 33 3 27 29 31 34 3 30 29 31 32 3 30 29 31 33 3 30 29 31 34 3 35 29 31 32 3 35 29 31 33 3 35 29 31 34 3 27 29 35 36 3 27 29 35 37 3 27 29 35 38 3 30 29 35 36 3 30 29 35 37 3 30 29 35 38 3 31 29 35 36 3 31 29 35 37 3 31 29 35 38 3 27 39 41 42 3 27 39 41 43 3 40 39 41 42 3 40 39 41 43 3 39 41 43 44 3 39 41 43 45 3 39 41 43 59 3 42 41 43 44 3 42 41 43 45 3 42 41 43 59 3 41 43 45 46 3 41 43 45 47 3 41 43 45 48 3 44 43 45 46 3 44 43 45 47 3 44 43 45 48 3 59 43 45 46 3 59 43 45 47 3 59 43 45 48 3 41 43 59 60 3 41 43 59 61 3 44 43 59 60 3 44 43 59 61 3 45 43 59 60 3 45 43 59 61 3 43 45 48 49 3 43 45 48 51 3 46 45 48 49 3 46 45 48 51 3 47 45 48 49 3 47 45 48 51 3 45 48 49 50 3 45 48 49 53 3 51 48 49 50 3 51 48 49 53 3 45 48 51 52 3 45 48 51 55 3 49 48 51 52 3 49 48 51 55 3 48 49 53 54 3 48 49 53 57 3 50 49 53 54 3 50 49 53 57 3 48 51 55 56 3 48 51 55 57 3 52 51 55 56 3 52 51 55 57 3 49 53 57 55 3 49 53 57 58 3 54 53 57 55 3 54 53 57 58 3 51 55 57 53 3 51 55 57 58 3 56 55 57 53 3 56 55 57 58 3 43 59 61 62 3 43 59 61 63 3 60 59 61 62 3 60 59 61 63 3 59 61 63 64 3 59 61 63 65 3 59 61 63 66 3 62 61 63 64 3 62 61 63 65 3 62 61 63 66 3 61 63 66 67 3 61 63 66 68 3 64 63 66 67 3 64 63 66 68 3 65 63 66 67 3 65 63 66 68 3 63 66 68 69 3 63 66 68 70 3 67 66 68 69 3 67 66 68 70 3 66 68 70 71 3 66 68 70 72 3 66 68 70 90 3 69 68 70 71 3 69 68 70 72 3 69 68 70 90 3 68 70 72 75 3 dih_ARG_chi1_N_C_C_C 90 70 72 75 3 dih_ARG_chi1_C_C_C_CO 68 70 72 73 3 68 70 72 74 3 71 70 72 73 3 71 70 72 74 3 71 70 72 75 3 90 70 72 73 3 90 70 72 74 3 68 70 90 91 3 68 70 90 92 3 71 70 90 91 3 71 70 90 92 3 72 70 90 91 3 72 70 90 92 3 70 72 75 76 3 70 72 75 77 3 70 72 75 78 3 73 72 75 76 3 73 72 75 77 3 73 72 75 78 3 74 72 75 76 3 74 72 75 77 3 74 72 75 78 3 72 75 78 79 3 72 75 78 80 3 72 75 78 81 3 76 75 78 79 3 76 75 78 80 3 76 75 78 81 3 77 75 78 79 3 77 75 78 80 3 77 75 78 81 3 75 78 81 82 3 75 78 81 83 3 79 78 81 82 3 79 78 81 83 3 80 78 81 82 3 80 78 81 83 3 78 81 83 84 3 78 81 83 87 3 82 81 83 84 3 82 81 83 87 3 81 83 84 85 3 81 83 84 86 3 87 83 84 85 3 87 83 84 86 3 81 83 87 88 3 81 83 87 89 3 84 83 87 88 3 84 83 87 89 3 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 5 25 23 24 1 improper_O_C_X_Y 23 27 25 26 1 improper_Z_N_X_Y 27 41 39 40 1 improper_O_C_X_Y 39 43 41 42 1 improper_Z_N_X_Y 43 61 59 60 1 improper_O_C_X_Y 45 48 51 49 1 improper_Z_CA_X_Y 48 53 49 50 1 improper_Z_CA_X_Y 48 55 51 52 1 improper_Z_CA_X_Y 49 57 53 54 1 improper_Z_CA_X_Y 51 57 55 56 1 improper_Z_CA_X_Y 53 55 57 58 1 improper_Z_CA_X_Y 59 63 61 62 1 improper_Z_N_X_Y 63 68 66 67 1 improper_O_C_X_Y 66 70 68 69 1 improper_Z_N_X_Y 70 91 90 92 1 improper_O_C_X_Y 78 83 81 82 1 improper_Z_N_X_Y 81 84 83 87 1 improper_O_C_X_Y 83 85 84 86 1 improper_Z_N_X_Y 83 88 87 89 1 improper_Z_N_X_Y ; Include Position restraint file #ifdef POSRES #include "posres.itp" #endif ; Include water topology #include "oplsaa.ff/spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "oplsaa.ff/ions.itp" [ system ] ; Name TEST in water [ molecules ] ; Compound #mols Protein 1 CL 2