AMBER Archive (2008)

Subject: AMBER: MM-PBSA and trajectory input

From: Arturas Ziemys (
Date: Thu Nov 13 2008 - 11:22:36 CST


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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