AMBER Archive (2008)

Subject: AMBER: Query on MM-PBSA

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Fri Jun 06 2008 - 00:46:32 CDT

Hi Amber Users,

I came a tutorial for MM-PBSA
(http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html). I am trying to
use both dephi version as well as the AMBER-PB solver. I get different
results. My ligand is charged and it is recommended to use delphi in
tutorial. But I think the pb-total is more consistent with gb-total
using the default pb solver but with delphi it is too negative. I m
using the last snapshot to calculate PBSA and GBSA.

I dont know what is going wrong. I would appreciate your guidance.

Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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