Comments (4)
jchodera
commented on June 15, 2024
Agreed! These files should all be deleted:
ANTECHAMBER_AC.AC
ANTECHAMBER_AC.AC0
ANTECHAMBER_BOND_TYPE.AC
ANTECHAMBER_BOND_TYPE.AC0
ATOMTYPE.INF
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davidlmobley
commented on June 15, 2024
Yes, please do. Overlooked those in my rush.
DM
On Fri, Sep 26, 2014 at 8:40 AM, John Chodera [email protected]
wrote:
Agreed! These files should all be deleted:
ANTECHAMBER_AC.AC
ANTECHAMBER_AC.AC0ANTECHAMBER_BOND_TYPE.AC
ANTECHAMBER_BOND_TYPE.AC0
ATOMTYPE.INF—
Reply to this email directly or view it on GitHub
#1 (comment).
David Mobley
[email protected]
949-385-2436
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kyleabeauchamp
commented on June 15, 2024
See #4
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kyleabeauchamp
commented on June 15, 2024
For the record, here's what I did:
- Fork repository (do this once) via web interface. This allows me to make changes in my own copy of the repo, which I then pull request to the choderalab version.
git clone [email protected]:kyleabeauchamp/FreeSolv.git
cd FreeSolv
git branch deletejunk
git checkout deletejunk
git rm ANTECHAMBER_* ATOMTYPE.INF
git commit -m "Deleted extra antechamber files."
git push origin deletejunk
Then file a pull request via the GitHub web interface.
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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
- 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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