AMBER: MM-PBSA and trajectory input

From: Arturas Ziemys <>
Date: Thu, 13 Nov 2008 11:22:36 -0600


I do analysis on peptide binding in protein. I have found that majority
of people use very short trajectories to feed for MM-PBSA calculations
(200-500 ps from different references). I compared MM-PBSA results and
realized that final dH is very sensitive to the particular segment of
trajectory is used to calculate binding energies. Also, it seems that
MM-PBSA method is very sensitive to the number of frames I use.

I understand problems of protein/peptide sampling. However, some values
dH fluctuate ~ 10 kcal/mol using different trajectory length or
different segment. I wander how to address that issue of guessing what
trajectory segment and length should be taken for MM-PBSA calculation ?

With best

Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929  
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Received on Fri Dec 05 2008 - 14:40:30 PST
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