AMBER Archive (2002)

Subject: entropy calculation

From: X. Tan (xjtan_at_u.washington.edu)
Date: Mon Jun 10 2002 - 18:42:59 CDT

dear amber users,

when I ran mm_pbsa, I got stucked in the nmode calculation. I have some
questions about it.

1. can I just calculated residues 8 A (or less)around the ligand? and is
that enough to give out the correct answer?

2. I need to do nmdoe calculations for complex, protein and ligand for
each snapshot or only one set?

I use amber6, and the memory is about 1G. I hope someone can give me some
hints or examples to run entropy calculation using nmode.
Thanks in advance.

Xiaojian