Can you help me with alanine scanning with AMBER?

06 June 2014 1 4K Report

From what I have understood (from the AMBER manual) I have to prepare the topology of every single mutant I want to scan and, subsequently, I have to start an individual run (with the MMPBSA.py program) for each of them.

I feel that this procedure is not a "scanning" at all.

Do you know any pipeline for AMBER? With "pipeline" I mean any automated workflow that, starting from a subset of residue, provides mutations and calculations as well (something like the web service provided with Robetta).

Bipin Singh

http://compbiochem.org/Software/compasm/Home.html

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