[AMBER] Decomposition of the MMGBSA based on multi trajectory input

From: James Starlight <jmsstarlight.gmail.com>
Date: Tue, 3 Mar 2015 12:58:44 +0100

Dear Amber users!

I'm going to perform per-residue decomposition analysis for several
protein-ligand systems having 3 independent trajectories for each
system. I wounded to know
1) is it possible to include several trajectories tax the standard
input to MMPBSA.py or alternatively I should to merge all trajectories
for the same system together using cpptraj?
2) what I should do if some of the trajectories for the same system
are consisted of different number of atoms (and its parm7 files also
differs)-> because each time each system has been solvated de novo->
so the number of solvent molecules in identical protein-ligand systems
are differs. In these regards Is it possible to i) strip all solvent
using cpptraj from each trajectory and ii) to join all of them
together ( consisted of only protein-ligand atoms) iii) to provide
stripped parm7 file for the MMPBSA.py as well as the stripped

I would be very thankful for any other solutions,


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Received on Tue Mar 03 2015 - 04:30:03 PST
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