AMBER Archive (2003)

Subject: AMBER: Nmode analysis ptn-ligand complex

From: Jory Zmuda (jzmuda_at_vt.edu)
Date: Tue Dec 16 2003 - 17:11:13 CST

Hello,

I am attempting to calculate the entropy of several protein-ligand
complexes (about 7800 atoms) after 1.5ns of MD. In several papers, it
notes that for large systems, only a small (8A) sphere around the ligand
is used in the calculation. I have used Carnal to determine the
residues within 8A of my ligand. I have also created a pdb file of
those residues and created prmtop and inpcrd files in leap. After I
perform a minimization and then run nmode, the calculated entropy is
about 1356 cal/mol-kelvin.

I don't think this is the correct/best approach. Can someone please
describe how one could calculate the entropy for a sphere of residues in
nmode after MD? 

-- 
Jory L. Zmuda
Graduate Student
Genetics, Bioinformatics and Computational Biology (GBCB)
Virginia Polytechnic Institute and State University
201 Engel Hall
Blacksburg, VA 24060
Phone - 540-231-9080

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