MobleyLab FreeSolv issues

MobleyLab / FreeSolv

Experimental and calculated small molecule hydration free energies

http://www.escholarship.org/uc/item/6sd403pz

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issues

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Is gromacs_energies available to download anywhere?

#52 xiaowei-xie2 opened 1 year ago
4
mobley_3323117 (sulfolane) has non-standard SMILES

#51 jchodera opened 1 year ago
1
gromacs-mdp:with verlet lists rcoulomb!= rvdw is not supported

#49 yuchen22 opened 3 years ago
3
Sanitize SDF files

#48 proteneer opened 4 years ago
0
Problems with processing some SMILES - omega returned error code 0

#47 kadiliissaar opened 4 years ago
0
rebuild_freesolv.py script

#46 kadiliissaar closed 4 years ago
2
Cannot generate GAFF mol2 from Tripos mol2 file

#45 jchodera closed 4 years ago
2
GAFF version

#44 nhenriksen opened 6 years ago
5
Update README.md to reflect release/Zenodo DOI for 0.52

#43 davidlmobley closed 6 years ago
0
Set up Travis-CI testing

#42 davidlmobley opened 7 years ago
0
Remove duplicate from database, update DOIs and other info

#41 davidlmobley closed 7 years ago
1
Potential duplicate molecules in FreeSolv Set

#40 bannanc closed 7 years ago
12
Update README.md with paper citation info.

#39 davidlmobley closed 7 years ago
0
Update README.md to reflect Zenodo DOI for latest release

#38 davidlmobley closed 7 years ago
0
Documentation clarifications and script update for directory naming

#37 davidlmobley closed 7 years ago
0
Changes from adding automated parameter conversion

#36 mrshirts closed 7 years ago
7
Make CHARMM input files via ParmEd

#35 davidlmobley opened 7 years ago
0
Fix for parsing IUPAC/nicknames

#34 nathanmlim closed 7 years ago
0
Update column names to be more informative

#33 jchodera opened 7 years ago
2
Repack the FreeSolv data as SD Data

#32 nathanmlim closed 7 years ago
0
Add iPython Notebooks which make a version of FreeSolv attached to OEMols

#31 nathanmlim closed 7 years ago
0
Updates to README.md

#30 davidlmobley closed 7 years ago
0
Flag molecules with possibly problematic tautomers (and investigate tautomers for them)?

#29 davidlmobley opened 7 years ago
0
Deposit new files for major rebuild of database

#28 davidlmobley closed 7 years ago
2
In next update, include a json format version of database

#27 davidlmobley closed 7 years ago
1
Add Zenodo to README.md

#26 davidlmobley closed 7 years ago
0
Migrate issues and close this repo?

#25 davidlmobley closed 7 years ago
10
Have GBSA models been benchmarked on FreeSolv?

#24 jchodera closed 7 years ago
4
Fixing issues with two SMILES strings for nitro-containing compounds

#23 davidlmobley closed 9 years ago
2
Protocol for generating solvated input files for various codes (AMBER, gromacs)

#22 jchodera opened 9 years ago
1
Strip water molecules from all topology/coordinate files in current database

#21 davidlmobley closed 7 years ago
8
Re-construct database files from primary data

#20 davidlmobley closed 7 years ago
11
Decide any other supporting files/data which ought to be captured when database is re-constructed from primary data

#19 davidlmobley closed 7 years ago
2
Decide what additional data we want pulled from the source literature/what instructions to give

#18 davidlmobley opened 9 years ago
0
Resolve issues relating to trajectory re-generation and re-calculation of hydration free energies

#17 davidlmobley closed 7 years ago
1
Re-compute hydration free energies for all compounds

#16 davidlmobley closed 7 years ago
1
Re-generate trajectories for all compounds - implicit solvent, explicit solvent, and vacuum

#15 davidlmobley closed 7 years ago
3
Should SDF files contain other fields from database?

#14 jchodera opened 9 years ago
2
Naming convention for 'title' record in Tripos mol2 files

#13 jchodera closed 7 years ago
5
Implement Bayly's recommended AM1-BCC charge assignment scheme

#12 jchodera closed 9 years ago
0
Implementing script to generate Bayly's preferred AM1-BCC charges

#11 jchodera closed 9 years ago
10
Removing redundant compound mobley_4689084, updating README.md

#10 davidlmobley closed 9 years ago
0
Which database format should store primary data?

#9 jchodera opened 9 years ago
2
Create Release for v0.31

#8 jchodera closed 9 years ago
3
Add a nickname column to database.txt

#7 leeping closed 9 years ago
12
mobley_352111 and mobley_4689084 are the same molecule

#6 leeping closed 9 years ago
9
[WIP] Updated README.md with markdown version of changelog.

#5 jchodera closed 10 years ago
1
Deleted extra antechamber files.

#4 kyleabeauchamp closed 10 years ago
7
Add scripts used to generate these files

#3 jchodera closed 9 years ago
6
Add source for v0.31_docs.pdf

#2 jchodera closed 9 years ago
6