https://github.com/becksteinlab/alchemical_conformational_analysis
https://github.com/becksteinlab/alchemical_conformational_analysis
Science Score: 13.0%
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Low similarity (5.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Becksteinlab
- Language: Jupyter Notebook
- Default Branch: main
- Size: 5.57 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Conformational Analysis of SAMPL7 molecules
Start with SM46 (see submitted paper).
Bogdan created timeseries for the two main dihedrals (see tar file on spudda, too big for repo).
To set up:
bash ./bin/RSYNC
bash ./bin/SETUP
You can then use the notebooks in analysis.
You need a conda environment with
- alchemlyb
- pandas
- matplotlib
- numpy
- tqdm
- seaborn
Raw data
Generated with gmx angle (see GROMACS_ANALYZE_dihedral_analysis):
bash
gmx angle -type dihedral -f $i/md.xtc -n $ff-dih1.ndx -od $j-dih1-dist.xvg -ov $j-dih1-ts.xvg
gmx angle -type dihedral -f $i/md.xtc -n $ff-dih2.ndx -od $j-dih2-dist.xvg -ov $j-dih2-ts.xvg
CGENFF and OPLS-AA (mol2ff)
Tar file with data.
* spudda.beckstein.physics.asu.edu:/nfs/homes/bogdan/Projects/SAMPL7-PhysProp/_dih_analysis.tgz
Use bin/RSYNC.sh to get the data.
GAFF and LigParGen
Shujie generated the data
yamsolo.beckstein.physics.asu.edu:/nfs/homes3/sfan/Projects/SAMPL7/_dih_gaffyamsolo.beckstein.physics.asu.edu:/nfs/homes3/sfan/Projects/SAMPL7/_dih_ligpargen
Owner
- Name: Becksteinlab
- Login: Becksteinlab
- Kind: organization
- Email: obeckste@asu.edu
- Location: Tempe, AZ
- Website: https://becksteinlab.physics.asu.edu
- Repositories: 56
- Profile: https://github.com/Becksteinlab
Computational Biophysics at Arizona State University
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