Protein-ligand Complex Parameterization

This program is to automatically generate parameterized protein-ligand complex for Molecular Dynamics simulation using antechamber or gromacs pdb2gmx.

Before running the code

The gromacs portion of the code doesn't work on Mac for echo behaves differently in Mac from Linux. The pdb2gmx manual entry fails to register in the Mac environment.

Set up the env

The environment can be easily built with conda via

conda env create -f env.yml

Load the env

The conda environment should be available to load with

source activate md_setup

Run the parameterization

The code takes in pdb files and builds topology according to the chosen force field. Examples can be found [here][https://github.com/hengma1001/complex_sim/tree/master/examples].

Inputs

It requires pdb file as input format. The amber function can automatically parameterize small molecule ligand with antechamber. The gmx function needs an additional entry to specify the force field path.

Running the code

The coda is simply running

python param_amber.py

after all the input path is specified in the script.