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Hi,
pyScoMotif is really a great tool for structural motif or pocket search! Actually, I've tried to find such a tool for a long time. Several tools have been found and compared, like COLLAPSE (h…
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### Bug summary
When I run gmx_mmpbsa, some error occurs.
### Terminal output
```bash
File "/lustre/user/lulab/lulabrotation/miniconda3/envs/gromacs/bin/gmx_MMPBSA", line 8, in
sys.exit(gm…
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Hi.
I am trying to get interaction fingerprint for a pair of proteins, from the PDB file with the structure of the complex.
I have created two mol files, after loading them into MDA.
`hla_selection…
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* **Suggested term label:**
* virus-like capsid
* **Definition (free text):**
* A protein coat that surrounds nucleic acid to form a structure similar to a virus capsid. Virus-like capsids a…
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### Bug summary
Hi,
I am trying to calculate the mmpbsa between a protein and peptide.
I used gromacs2023.02 and the pbc was removed from the trajectory. But since the version of gmx_MMPBSA is co…
yesyb updated
4 months ago
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**Submitting author:** @JonnyTran (Nhat Tran)
**Repository:** https://github.com/BioMeCIS-Lab/OpenOmics
**Version:** v0.8.8
**Editor:** @arfon
**Reviewers:** @arfon
**Managing EiC:** Arfon Smith
**:…
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Hi,
I am facing the following error, while running the job via command line.
**FileNotFoundError: [Errno 2] No such file or directory: '/home/medicina/Downloads/DynamicBind/workdir/big_score_model…
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### Bug summary
Error occurs when converting topology files. Amber forcefields are used from charmm-gui webserver. The error is about the pairs func, and I assume in particular from the glycopyranose…
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I've set up a conda environment (Miniconda, python 3.10, latest alphafold (2.3.2) and alphapulldown (1.0.3) plus all dependencies according to the specifications). This seems to work well and it gener…
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Hello there,
Can you guys help me to get the contacts of a trajectory ensemble?
The ensemble consist of a trajectory of molecular dynamics with a protein + ligand complex.
chain that represents …