AMBER Archive (2005)

Subject: AMBER: PBSA residual and pairwise decompostion

From: Jiten (jiten_at_postech.ac.kr)
Date: Tue Jan 25 2005 - 07:43:38 CST

Dear all,

I tried to calculated the residue and pairwise decomposition using DCTYPE =2 and 4 options. I have notice some irregularity in the result. I tried to find the free energy contribution for the drug binding to the protein active site (It is drug-258, only ligand residue in the complex as in the enclosed excel file).

1. In pairwise data all the B-terms (backbone) are displayed as 0 (zero), while it shows some number in the case of residue decompostion data. Despite this the TVDW, TELE and TGAS values are the same in both the cases.

2. The most drastic differences are in GB calculations. The residue decompposition calculation seems to be alright as the total of the sum of the energy values of the residue is same with of the free energy binding calculated using MM-PBGB.

Therefore, I wonder if the energy values reported for pairwiase decomposition may be right or wrong.

Your valuable suggestions/corrections on this regard will be highly appreciated.

Sincerely,

N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
Home Page : http://www.geocities.com/njs_19


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