AMBER Archive (2008)

Subject: RE: AMBER: MM_PBSA snapshot statistic calc problem

From: Peterson, Matthew W. (mpeterson_at_mitre.org)
Date: Mon Sep 29 2008 - 16:25:57 CDT

I’ve run into the same problems as well, along with some others that I
didn’t run into using Amber 9

 

Matt

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
Behalf Of Vasu Chandrasekaran
Sent: Monday, September 29, 2008 3:08 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: MM_PBSA snapshot statistic calc problem

 

If the snapshot_statistics.out file is not generated automatically, you
can manually generate the statistics output from your mmpbsa
calculations using the mm_pbsa_statistics.pl executable (a perl script)
found in the mm_pbsa directory (I think it will be under amber/src/).

Use the snapshot_statistics dot in as the input file, assign an output
file and if you have the snapshots of com, rec and lig from three
different trajectories, set calc_delta = 2. If you had extracted the
snapshots from the same trajectory, set calc_delta = 1. For both cases,
you can set calc_decomp to 0.

Hope that helps.

Vasu

2008/9/27 haixiao jin <jinhx952_at_gmail.com>

dear Hannes，

I have the same problem.

have you solved it ?

or any other amber users can give us some suggestion to solve this
problem ?

thank you!

On Tue, Aug 5, 2008 at 8:45 PM, Hannes Wallnoefer
<Hannes.Wallnoefer_at_uibk.ac.at> wrote:

Hi amber-users,

I have a problem with the MM_PBSA tool in amber. To be sure that it is
not
related to my system i downloaded the snapshots and the input files of
the
tutorial A3: MM_PBSA.
When i perform the MM_PBSA calculation everything seems to be fine, but
in the
end the error: No data for 0+0 PB ELRAELE 0 appears and there is no
snapshots_statistics.out file. In the log-file the
mesage: WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
is found for every snapshot. I attached the log-file and the out-files
with all
of the calculated values.
Can anybody assist me with this problem?

Greetings
Hannes

  

-- 
Vasu Chandrasekaran
UNC-Chapel Hill 
Ph: 706-296-7894 (Cell)
URL: http://vasu.myweb.uga.edu

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