Mercurial > repos > chemteam > gmx_fep
diff alchemical_run/test-data/morph.top @ 0:19d1d4c30402 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
| author | chemteam |
|---|---|
| date | Mon, 11 Nov 2019 13:20:39 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/morph.top Mon Nov 11 13:20:39 2019 -0500 @@ -0,0 +1,232 @@ +; 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 +