Comments (2)
jchodera
commented on July 19, 2024
It looks like the scripts/rebuild_freesolv.py script relies on openmoltools, which is pretty fragile and hasn't always remained backwards-compatible:
https://github.com/choderalab/openmoltools
We've been hoping to replace all this functionality with more modern tools in the openforcefield toolkit and OpenMM, but haven't yet updated the FreeSolv repo yet.
It looks like the default behavior of get_charges() changed at some point to no longer retain the conformers generated during the charging process.
You should be able to just change this line from
charged = openmoltools.openeye.get_charges(molecule)to
charged = openmoltools.openeye.get_charges(molecule, keep_confs=1)and you'll have a conformer!
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kadiliissaar
commented on July 19, 2024
Yes, this solves the problem - thanks a lot!
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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
- GAFF version HOT 5
- Cannot generate GAFF mol2 from Tripos mol2 file 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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