Remove invalid water-containing PDB files (and associated AMBER input…

…s which are not used); add new water-containing input PDB files; add README.md documentating origin of solvated boxes.
openforcefield · Mar 24, 2017 · 9094408 · 9094408
1 parent 1ff1b51
commit 9094408
Show file tree

Hide file tree

Showing 18 changed files with 10,701 additions and 18,170 deletions.
diff --git a/smarty/data/systems/README.md b/smarty/data/systems/README.md
@@ -0,0 +1,3 @@
+Solvated systems here were built using SolvationToolkit (github.com/mobleylab/solvationtoolkit) version 0.41 and 0.42 (equivalent except for DOI assignment for the latter), except as noted.
+
+Because of a bug in handling of insertion of CONECT entries in SolvationToolkit/openmoltools for systems containing water, water boxes were generated by taking GROMACS coordinate/topology files for solvated cyclohexane ('mobley_2689721') and ethanol ('mobley_2310185') from FreeSolv 0.5 and converting to PDB format via OpenMM 7.1 (reading via GromacsGroFile and GromacsTopFile and writing via PDBFile). 
diff --git a/smarty/data/systems/amber/butanol_water_1_300.inpcrd b/smarty/data/systems/amber/butanol_water_1_300.inpcrd
diff --git a/smarty/data/systems/amber/butanol_water_1_300.prmtop b/smarty/data/systems/amber/butanol_water_1_300.prmtop
diff --git a/smarty/data/systems/amber/cyclohexane_water_1_300.inpcrd b/smarty/data/systems/amber/cyclohexane_water_1_300.inpcrd
diff --git a/smarty/data/systems/amber/cyclohexane_water_1_300.prmtop b/smarty/data/systems/amber/cyclohexane_water_1_300.prmtop
diff --git a/smarty/data/systems/amber/ethanol_water_1_300.inpcrd b/smarty/data/systems/amber/ethanol_water_1_300.inpcrd
diff --git a/smarty/data/systems/amber/ethanol_water_1_300.prmtop b/smarty/data/systems/amber/ethanol_water_1_300.prmtop
diff --git a/smarty/data/systems/amber/methanol_water_1_300.inpcrd b/smarty/data/systems/amber/methanol_water_1_300.inpcrd
diff --git a/smarty/data/systems/amber/methanol_water_1_300.prmtop b/smarty/data/systems/amber/methanol_water_1_300.prmtop
diff --git a/smarty/data/systems/amber/propanol_water_1_300.inpcrd b/smarty/data/systems/amber/propanol_water_1_300.inpcrd
diff --git a/smarty/data/systems/amber/propanol_water_1_300.prmtop b/smarty/data/systems/amber/propanol_water_1_300.prmtop
diff --git a/smarty/data/systems/packmol_boxes/butanol_water_1_300.pdb b/smarty/data/systems/packmol_boxes/butanol_water_1_300.pdb
diff --git a/smarty/data/systems/packmol_boxes/cyclohexane_water.pdb b/smarty/data/systems/packmol_boxes/cyclohexane_water.pdb
diff --git a/smarty/data/systems/packmol_boxes/cyclohexane_water_1_300.pdb b/smarty/data/systems/packmol_boxes/cyclohexane_water_1_300.pdb
diff --git a/smarty/data/systems/packmol_boxes/ethanol_water.pdb b/smarty/data/systems/packmol_boxes/ethanol_water.pdb
diff --git a/smarty/data/systems/packmol_boxes/ethanol_water_1_300.pdb b/smarty/data/systems/packmol_boxes/ethanol_water_1_300.pdb
diff --git a/smarty/data/systems/packmol_boxes/methanol_water_1_300.pdb b/smarty/data/systems/packmol_boxes/methanol_water_1_300.pdb
diff --git a/smarty/data/systems/packmol_boxes/propanol_water_1_300.pdb b/smarty/data/systems/packmol_boxes/propanol_water_1_300.pdb
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		Solvated systems here were built using SolvationToolkit (github.com/mobleylab/solvationtoolkit) version 0.41 and 0.42 (equivalent except for DOI assignment for the latter), except as noted.

		Because of a bug in handling of insertion of CONECT entries in SolvationToolkit/openmoltools for systems containing water, water boxes were generated by taking GROMACS coordinate/topology files for solvated cyclohexane ('mobley_2689721') and ethanol ('mobley_2310185') from FreeSolv 0.5 and converting to PDB format via OpenMM 7.1 (reading via GromacsGroFile and GromacsTopFile and writing via PDBFile).