AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa_statistical.pl

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Wed Aug 30 2006 - 12:52:56 CDT

Hi, William,

If you want to calculate the deltaG, use 1 for "calc delta". If you do not
decompose energy terms (DC), use 0 for "calc decomp", use 1 for "calc
decomp" if you use DC and DCTYPE is 1 or 2, use 2 for "calc decomp" if
DCTYPE is 3 or 4. You should have a file called *_statistics.in, which
contains three lines like
*_com.all.out
*_rec.all.out
*_lig.all.out
Make sure these three files are complete. Then you can use
mm_pbsa_statistics.pl 1 0 *_statistics.in test.out
to get your results. (I assume you don't decompose energy)

Hope it helps.

Jianyin

On 8/29/06, William Wei <william.wei_at_utoronto.ca> wrote:
>
> Dear all,
>
> I was using mm_pbsa to calculate the deltaG. By some reason it stopped at
> statistical accounting. Because it took a long time to finish the free
> energy for my snapshots. I have the output for Com. Rec. and Lig. from
> mmpbsa. What is the command for "mm_pbsa_statistical"?
>
> usage: mm_pbsa_statistics.pl <calc delta ? 0..1> <input file> <output
> file>
>
> what is the first parameter "calc delta ? 0..1". If I have 100 snapshots
> for Com, rec. and lig. what is my input?
>
> Anybody used that? Thanks in advance,
> William
>
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