[AMBER] question about advanced tutorial 3

From: Mohsen Zakeri <mohsen.zakery.gmail.com>
Date: Fri, 10 Jul 2015 14:42:03 +0430


I am a new AmberTools user and I am trying to calculate the binding energy
of Protein-Ligand using AmberTools. In order to do that I am trying to
learn from advanced Tutorial #3 (TUTORIAL A3: MM-PBSA
<http://ambermd.org/tutorials/advanced/tutorial3/index.htm>). It has been
said there that we should separate ras-raf.pdb into to 2 pdb files
"ras.pdb" and "raf.pdb", but I do not know how I can do so, can you help me
with this separation part? Can I do that using Amber?


Mohsen Zakeri, B.Sc.
ECE Department, Computer Engineering
University of Tehran, Tehran, Iran
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Received on Fri Jul 10 2015 - 03:30:03 PDT
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