[gmx-users] gmxpbsa -protein-DNA

Dear all, I am trying to run gmxpbsa for my protein-DNA complex. The problem is that I am getting very high energies in the final MMPBSA file: Number of frames= 20 Overall Coulombic =-24244.152+/-38.102 kJ/mol Overall Lennard-Jones

Re: [gmx-users] GMXPBSA

Hi, Please have look here: GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning http://www.sciencedirect.com/science/article/pii/S0010465514003154? Contact me in private if you need help Best And Il 20/lug/2015 16:19 Urszula Uciechowska ha scritto: Dear gromacs

[gmx-users] GMXPBSA

Dear gromacs users, I would like to run BFE calculations with gromacs. I performed MD simulations for 100ns and would like to extract snapshots from the MD and split them into the complex, protein and DNA. My question is how many sps should I extarct from the MD? and Are there any scripts availa