LigParGenTools

Scripts to set up condensed phase simulations using of LigParGen Server

Most of the FF such as AMBER, OPLS-AA and CHARMM are built using bottom up approach i.e, they are parameterized to reproduce condensed phase properties of organic building blocks of macromolecules. To validate the performance of these force fields one need to look at their performance in reproducing pure liquid properties. Creation of custom solvent boxes of desired size with desired number of solvent molecules is the first step in doing pure liquid simulations. This script is created for this purpose.

1. Steps to setup Pure liquid simulations

1. Choose NAMD, Gromacs or OpenMM for your simulation
2. Get parameter and topology files for solvent molecules (1-Octanol) using LigParGen Server
3. Create a box of Octanol using CustomSolBox.py using python CustomSolBox.py -p OCT.pdb -b 65 -r OCT
4. Minimize the box and do NPT Equibration for 2 nano seconds to get a good box. python PLIQ_OPENMM.py