NAMD-MD

Reminder

You can finish all the process in google colab, the difference to a local procedure would be you need run some command in terminal. Another reminder is you should remove the duplicated chain before dive into topology generation.

Fix protein problems with PDBfixer

use https://colab.research.google.com/drive/1bkVMue-ndnI1TIvwNRGbpmpV5tiz-FN5#scrollTo=O1LuW0KNOGQJ to keep only one chain (fixer.removeChains(chainIds='B')), and fix other problems like atom missing etc.

This repository try to introduce molecular dynamics of protein-ligand complex to more people, especially those beginners, with all open-souuced resouces. VMD (https://www.ks.uiuc.edu/), NAMD (https://www.ks.uiuc.edu/) and py3Dmol (https://github.com/avirshup/py3dmol), as well as open babel (https://github.com/openbabel/openbabel) are the main components contained in this protocal. The force file package used is charmm as per https://www.charmm.org/charmm/resources/charmm-force-fields/ for protein, small moleucles are paramerized by web server LigPargen (http://zarbi.chem.yale.edu/ligpargen/).

This is designed only for learning purpose, anyone with commercial purpose might need to check out by themself if they need a commercial license in relation to some certain package, even these are all "open source".

Usage

It is assumed you already got anaconda installed on your linux computer, visit https://docs.anaconda.com/# to get one if not installed.

git clone https://github.com/quantaosun/NAMD-MD

cd NAMD-MD

Create a new Conda environment named "NAMD-MD"

conda create -n NAMD-MD python=3.7

Activate the new environment

conda activate NAMD-MD

In the new environment, install jupyter notebook

conda install jupyter

Start jupyter notebook and run the "NAMD-MD_local.ipynb"

jupyter notebook NAMD-MD_local.ipynb

If you have problem opening jupyter notebook in your "NAMD-MD" environment, try

conda remove jupyter

sudo apt install jupyter

jupyter notebook