[AMBER] MMGBSA residue-wise decomposition

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Wed, 7 Mar 2012 10:48:28 +0530

Dear Amber users,

As per the manual idecomp 3 - Pairwise decomp with 1-4 terms added to
internal potential terms
4 - Pairwise decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW
potential terms.

For my system when i did with idecomp 3 & 4 , in both cases, the internal
potential term was 0.000 +/- 0.000. and the total energy contribution of
the residues are different.

1. Is my calculation correct?
2. which method of decomposition should i use?
3. what is the reason for different total energy contribution of each
residue by different decomposition terms?

Please Clarify my doubts.

Thank you very much in advance

Rajeswari A
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Received on Tue Mar 06 2012 - 21:30:03 PST
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