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view alchemical_run/test-data/morph.top @ 0:5f136e371f44 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit 4c75f8d26505d221d4144f4ae7d2fb7698fbe4ab"
| author | chemteam |
|---|---|
| date | Mon, 18 Nov 2019 09:52:20 -0500 |
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; Gromacs Topology File written by Sire ; File written 05/01/19 13:21:14 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.833333 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon Cl- 17 35.453000 0.000000 A 0.447766 0.148913 HW 1 1.007940 0.000000 A 0.000000 0.000000 Na+ 11 22.989770 0.000000 A 0.243928 0.365846 OW 8 15.999400 0.000000 A 0.315075 0.635968 c3 6 12.010700 0.000000 A 0.339771 0.451035 ca 6 12.010700 0.000000 A 0.331521 0.413379 ha 1 1.007940 0.000000 A 0.262548 0.067362 hc 1 1.007940 0.000000 A 0.260018 0.087027 hc_du 0 0.000000 0.000000 A 0.000000 0.000000 [ moleculetype ] ; name nrexcl CL 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 Cl- 1 CL CL 1 -1.000000 35.450000 [ moleculetype ] ; name nrexcl Merged_Molecule 3 [ atoms ] ; nr type0 resnr residue atom cgnr charge0 mass0 type1 charge1 mass1 1 ca 1 LIG C 1 -0.130000 12.010000 ca -0.075744 12.010000 2 ca 1 LIG C1 2 -0.130000 12.010000 ca -0.129444 12.010000 3 ca 1 LIG C2 3 -0.130000 12.010000 ca -0.131444 12.010000 4 ca 1 LIG C3 4 -0.130000 12.010000 ca -0.131444 12.010000 5 ca 1 LIG C4 5 -0.130000 12.010000 ca -0.129444 12.010000 6 ca 1 LIG C5 6 -0.130000 12.010000 ca -0.075744 12.010000 7 ha 1 LIG H 7 0.130000 1.008000 c3 -0.053744 12.010000 8 ha 1 LIG H1 8 0.130000 1.008000 ha 0.129056 1.008000 9 ha 1 LIG H2 9 0.130000 1.008000 ha 0.130056 1.008000 10 ha 1 LIG H3 10 0.130000 1.008000 ha 0.130056 1.008000 11 ha 1 LIG H4 11 0.130000 1.008000 ha 0.129056 1.008000 12 ha 1 LIG H5 12 0.130000 1.008000 c3 -0.053744 12.010000 13 hc_du 1 LIG H 13 0.000000 1.008000 hc 0.043756 1.008000 14 hc_du 1 LIG H1 14 0.000000 1.008000 hc 0.043756 1.008000 15 hc_du 1 LIG H2 15 0.000000 1.008000 hc 0.043756 1.008000 16 hc_du 1 LIG H7 16 0.000000 1.008000 hc 0.043756 1.008000 17 hc_du 1 LIG H8 17 0.000000 1.008000 hc 0.043756 1.008000 18 hc_du 1 LIG H9 18 0.000000 1.008000 hc 0.043756 1.008000 [ bonds ] ; ai aj funct parameters 1 2 1 0.1398 316812 0.1398 316812 1 6 1 0.1398 316812 0.1398 316812 1 7 1 0.1086 331122 0.1516 209451 2 3 1 0.1398 316812 0.1398 316812 2 8 1 0.1086 331122 0.1086 331122 3 4 1 0.1398 316812 0.1398 316812 3 9 1 0.1086 331122 0.1086 331122 4 5 1 0.1398 316812 0.1398 316812 4 10 1 0.1086 331122 0.1086 331122 5 6 1 0.1398 316812 0.1398 316812 5 11 1 0.1086 331122 0.1086 331122 6 12 1 0.1086 331122 0.1516 209451 7 13 1 0.1097 314553 0.1097 314553 7 14 1 0.1097 314553 0.1097 314553 7 15 1 0.1097 314553 0.1097 314553 12 16 1 0.1097 314553 0.1097 314553 12 17 1 0.1097 314553 0.1097 314553 12 18 1 0.1097 314553 0.1097 314553 [ pairs ] ; ai aj funct 1 4 1 1 9 1 1 11 1 1 16 1 1 17 1 1 18 1 2 5 1 2 10 1 2 12 1 2 13 1 2 14 1 2 15 1 3 6 1 3 7 1 3 11 1 4 8 1 4 12 1 5 7 1 5 9 1 5 16 1 5 17 1 5 18 1 6 8 1 6 10 1 6 13 1 6 14 1 6 15 1 7 8 1 7 12 1 8 9 1 9 10 1 10 11 1 11 12 1 [ angles ] ; ai aj ak funct parameters 1 2 3 1 120.02 575.718 120.02 575.718 1 2 8 1 119.88 407.522 119.88 407.522 1 6 5 1 120.02 575.718 120.02 575.718 1 6 12 1 119.88 407.522 120.77 548.941 1 7 13 1 110.47 395.806 110.47 395.806 1 7 14 1 110.47 395.806 110.47 395.806 1 7 15 1 110.47 395.806 110.47 395.806 2 1 6 1 120.02 575.718 120.02 575.718 2 1 7 1 119.88 407.522 120.77 548.941 2 3 4 1 120.02 575.718 120.02 575.718 2 3 9 1 119.88 407.522 119.88 407.522 3 2 8 1 119.88 407.522 119.88 407.522 3 4 5 1 120.02 575.718 120.02 575.718 3 4 10 1 119.88 407.522 119.88 407.522 4 3 9 1 119.88 407.522 119.88 407.522 4 5 6 1 120.02 575.718 120.02 575.718 4 5 11 1 119.88 407.522 119.88 407.522 5 4 10 1 119.88 407.522 119.88 407.522 5 6 12 1 119.88 407.522 120.77 548.941 6 1 7 1 119.88 407.522 120.77 548.941 6 5 11 1 119.88 407.522 119.88 407.522 6 12 16 1 110.47 395.806 110.47 395.806 6 12 17 1 110.47 395.806 110.47 395.806 6 12 18 1 110.47 395.806 110.47 395.806 13 7 14 1 107.58 326.352 107.58 326.352 13 7 15 1 107.58 326.352 107.58 326.352 14 7 15 1 107.58 326.352 107.58 326.352 16 12 17 1 107.58 326.352 107.58 326.352 16 12 18 1 107.58 326.352 107.58 326.352 17 12 18 1 107.58 326.352 107.58 326.352 [ dihedrals ] ; ai aj ak al funct parameters 1 2 3 4 1 180 15.167 2 180 15.167 2 1 2 3 9 1 180 15.167 2 180 15.167 2 1 3 2 8 4 180 4.6024 2 180 4.6024 2 1 5 6 12 4 180 4.6024 2 0 0 2 1 6 5 4 1 180 15.167 2 180 15.167 2 1 6 5 11 1 180 15.167 2 180 15.167 2 1 6 12 16 1 0 0 0 0 0 0 1 6 12 17 1 0 0 0 0 0 0 1 6 12 18 1 0 0 0 0 0 0 2 1 6 5 1 180 15.167 2 180 15.167 2 2 1 6 12 1 180 15.167 2 180 15.167 2 2 1 7 13 1 0 0 0 0 0 0 2 1 7 14 1 0 0 0 0 0 0 2 1 7 15 1 0 0 0 0 0 0 2 3 4 5 1 180 15.167 2 180 15.167 2 2 3 4 10 1 180 15.167 2 180 15.167 2 2 4 3 9 4 180 4.6024 2 180 4.6024 2 2 6 1 7 4 180 4.6024 2 180 4.6024 2 3 2 1 6 1 180 15.167 2 180 15.167 2 3 2 1 7 1 180 15.167 2 180 15.167 2 3 4 5 6 1 180 15.167 2 180 15.167 2 3 4 5 11 1 180 15.167 2 180 15.167 2 3 5 4 10 4 180 4.6024 2 180 4.6024 2 4 3 2 8 1 180 15.167 2 180 15.167 2 4 5 6 12 1 180 15.167 2 180 15.167 2 4 6 5 11 4 180 4.6024 2 180 4.6024 2 5 4 3 9 1 180 15.167 2 180 15.167 2 5 6 1 7 1 180 15.167 2 180 15.167 2 5 6 1 12 4 0 0 2 180 4.6024 2 5 6 12 16 1 0 0 0 0 0 0 5 6 12 17 1 0 0 0 0 0 0 5 6 12 18 1 0 0 0 0 0 0 6 1 2 8 1 180 15.167 2 180 15.167 2 6 1 7 13 1 0 0 0 0 0 0 6 1 7 14 1 0 0 0 0 0 0 6 1 7 15 1 0 0 0 0 0 0 6 5 4 10 1 180 15.167 2 180 15.167 2 7 1 2 8 1 180 15.167 2 180 15.167 2 7 1 6 12 1 180 15.167 2 180 15.167 2 8 2 3 9 1 180 15.167 2 180 15.167 2 9 3 4 10 1 180 15.167 2 180 15.167 2 10 4 5 11 1 180 15.167 2 180 15.167 2 11 5 6 12 1 180 15.167 2 180 15.167 2 [ moleculetype ] ; name nrexcl NA 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 Na+ 1 NA NA 1 1.000000 22.990000 [ moleculetype ] ; name nrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834000 16.000000 2 HW 1 WAT H1 2 0.417000 1.008000 3 HW 1 WAT H2 3 0.417000 1.008000 #ifdef FLEXIBLE #else [ settles ] ; OW funct doh dhh 1 1 0.09572 0.15136 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif [ system ] BioSimSpace System [ molecules ] ;molecule name nr. Merged_Molecule 1 NA 5 CL 5 WAT 2151