Mercurial > repos > chemteam > gmx_trj
diff test-data/topol_md.top @ 7:16fad30d566a draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
| author | chemteam |
|---|---|
| date | Wed, 29 Sep 2021 07:42:39 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/topol_md.top Wed Sep 29 07:42:39 2021 +0000 @@ -0,0 +1,910 @@ +; +; 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