quantaosun/namd-md

Open Source, Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.

NAMD-MD

This repository tries to introduce molecular dynamics of the protein-ligand complex to more people, especially those beginners, with all open-sourced resources.

• VMD (https://www.ks.uiuc.edu/),
• NAMD (https://www.ks.uiuc.edu/) and
• py3Dmol (https://github.com/avirshup/py3dmol)
• Open babel (https://github.com/openbabel/openbabel)
• Charmm as per https://www.charmm.org/charmm/resources/charmm-force-fields/ for protein
• LigPargen (http://zarbi.chem.yale.edu/ligpargen/).

Usage

There are two ways you could use this workflow,

1. Run this procedure on Colab directly where all dependencies are installed on the fly each time you use it

2. Locally use after installing all dependencies by yourself.

namd-md's Issues

Topology DIHIDRAL error

In case you get this error during psfgen step

Please open top_all36_prot.rtf and comment out line 92 then modify the psfgenscript to add one more line.

topology ...
segment {
..
}
regenerate angles dihedrals # add this line to vmd script but delete that from protein topology top_all36_prot.rtf
writepsf psf-complext.psf
writepdb psf-complex.pdb

For a similar discussion, have a look at https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28692.html