AMBER Archive (2006)

Subject: AMBER: MMPBSA problem

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Fri Jun 09 2006 - 04:48:50 CDT

Dear amber users

I am calculating the binding energy of peptide-enzyme with mmpbsa, but
acctually I am new for mmpbsa so my 2 problems is ,first, how many snapshots
did I should make ? if my trajectories is 500 ps about 5000 frames
(0.2pstime step) since the ras-raf tutorial you set to 5 but why ?
That is the
first problem and the second problem is what kind of trajectories used to
generate the snapshots ? Is it average structure or the entire
trajectories including heat and equilibrate trajectories ? please help me
understood this.

Thank you in advance

Best regard

Jitrayut Jitonnom, Ph.D.
CSML
Chiang Mai University
Thailand
50200

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