AMBER Archive (2008)

Subject: AMBER: MM-PBSA and trajectory input

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Thu Nov 13 2008 - 11:22:36 CST

Hi,

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 

-- 

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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