[AMBER] Normal Mode Analysis in Amber

From: Robert DeLisle <rkdelisle.gmail.com>
Date: Wed, 21 Mar 2018 20:59:24 -0600

I'm working on a project in which I would like to perform Normal Mode
Analysis to explore conformations of a small protein. There are various
tools out there to do this, but I would also like to analyze the resulting
trajectory file using PCAsuite (http://mmb.pcb.ub.es/software
/pcasuite/pcasuite.html). PCAsuite uses Amber trajectory files as inputs
and creates a number of very useful outputs.

I cannot, however, find any information about how to perform Normal Mode
Analysis using Amber without running a full MD simulation first. Ideally, I
would be able to simply run NMA and write out a trajectory file suitable
for input to PCAsuite.

Any guidance to accomplish this is greatly appreciated.
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Received on Wed Mar 21 2018 - 20:00:03 PDT
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