AMBER Archive (2004)

Subject: Re: AMBER: how to use mm_pbsa_statistics.pl independently

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue Apr 13 2004 - 12:06:43 CDT


> Jufang Shan schrieb:
>
> Hi,
>
> I want to calculate the binding free energy between receptor and
> ligand. I calculated the entropy for the complex, receptor and ligand
> using normal mode separately since the same parameters don't work for
> all. My question is what value shall I give to "calc delta" (?0..1)
> and "calc decomp" (?0..2) to run mm_pbsa_statistics.pl? I am using
> Amber 7.

If the snapshots of com, rec, lig are from three different trajectories,
use calc_delta = 2. If the snapshots were extracted from the same
trajectory, use calc_delta = 1. For both cases, set calc_decomp to 0.

Best regards

Holger

>
> Thanks,
> Jufang
>
> ----------------------------------------------------------------
> Jufang Shan
> Graduate Student
> Dept. of Structural Biology
> St. Jude Children's Research Hospital
> Interdisciplinary Program
> The University of Tenessee Health Science Center

-- 
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Dr. Holger Gohlke
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