[AMBER] ratio between frames for MM/PBSA and frames for normal mode calculations

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Thu, 17 Oct 2013 02:10:54 +0300

Greetings,

I want to estimate the free energy o binding of a ligand to a protein by
using MM/PBSA and normal modes to estimate the entropy change. However, the
latter is very time consuming so I'd rather use a frame interval
(nminterval parameter) for that calculation. What would be an acceptable
ratio between the frames to do MM/PBSA and those to do normal modes? For
instance I want to do MM/PBSA on 6000 frames, then what would be a
reasonable number of frames to do normal mode analysis?

thanks,
Thomas

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
          tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Oct 16 2013 - 16:30:03 PDT