Comments (5)
davidlmobley
commented on July 19, 2024
2
@gduarter - do we say this anywhere? If not we may need to update the README.md here to clarify.
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nhenriksen
commented on July 19, 2024
2
@gduarter thanks for the info! Would be great if you added it here so that there is no ambiguity.
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davidlmobley
commented on July 19, 2024
1
@gduarter - can you comment on this?
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gduarter
commented on July 19, 2024
@nhenriksen - We used GAFF 1.7 (DOI: 10.1021/acs.jced.7b00104; section "Update of FreeSolv, the Free Community Solvation Free Energy Database", subsection "Method Details", in the last paragraph.)
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gduarter
commented on July 19, 2024
@dmobley - We say it in the 2017 paper, section "Update of FreeSolv, the Free Community Solvation Free Energy Database", subsection "Method Details", in the last paragraph.
It is not a bad idea to include it here as well, though.
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Related Issues (20)
- Decide any other supporting files/data which ought to be captured when database is re-constructed from primary data HOT 2
- Re-construct database files from primary data HOT 11
- Strip water molecules from all topology/coordinate files in current database HOT 8
- Protocol for generating solvated input files for various codes (AMBER, gromacs) HOT 1
- Have GBSA models been benchmarked on FreeSolv? HOT 4
- Migrate issues and close this repo? HOT 10
- In next update, include a json format version of database HOT 1
- Flag molecules with possibly problematic tautomers (and investigate tautomers for them)?
- Update column names to be more informative HOT 2
- Make CHARMM input files via ParmEd
- Potential duplicate molecules in FreeSolv Set HOT 12
- Set up Travis-CI testing
- Cannot generate GAFF mol2 from Tripos mol2 file HOT 2
- rebuild_freesolv.py script HOT 2
- Problems with processing some SMILES - omega returned error code 0
- Sanitize SDF files
- gromacs-mdp:with verlet lists rcoulomb!= rvdw is not supported HOT 3
- mobley_3323117 (sulfolane) has non-standard SMILES HOT 1
- Is gromacs_energies available to download anywhere? HOT 4
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