>===== Original Message From "X. Tan" <xjtan_at_u.washington.edu> =====
>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?
No.
>
>2. I need to do nmdoe calculations for complex, protein and ligand for
>each snapshot or only one set?
One is the minimum; may people would evaluate five snapshots or so, to
see how the entropy estimate varies.
..good luck...dac
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA |
http://www.scripps.edu/case
==================================================================
Received on Tue Jun 11 2002 - 06:56:37 PDT
