Re: [AMBER] Normal mode entropy calculations for active site residues

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Wed, 7 Jun 2017 04:18:05 +0000

HI,

Why don't you try entropy calculations using mm_pbsa.pl or mm_pbsa.py?





                   Best Regards

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Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy


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________________________________
From: Manjula Saravanan <manjusimba.gmail.com>
Sent: 07 June 2017 07:52:01
To: amber.ambermd.org
Subject: [AMBER] Normal mode entropy calculations for active site residues

Dear Sir/Madam,
         I have run 50ns MD for a ligand-protein complex. I need to
calculate the entropy of binding for this complex. I want some help for
preparing input files for normal mode calculation restricted around the
residues in the active site (<10-12 angstroms). I have no idea about how to
prepare the input files(all including nmode.in , .prmtop and .mdcrd) for
this kind of nmode calculation. I kindly ask for help around here. I hope
someone will give me a hand.
*With Best Regards*
*S. Manjula*
*Research Scholar*
*Laboratory of Biocrystallography and Computational Molecular Biology*
*Department of Physics*
*Periyar University*
*Salem-11*
*Tamilnadu*
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Received on Tue Jun 06 2017 - 21:30:02 PDT