I am using Amber 12. I do not know which bug fixes have been applied (I am running on the University of Pittsburgh Department of Computational and Systems Biology computing cluster. I would imagine all the appropriate bug fixes have been applied).
-Aaron
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, August 06, 2013 5:08 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Trajectory post-processing
Hi,
Which version of Amber are you using, and what bugfixes have been applied?
On Tue, Aug 6, 2013 at 2:50 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
>The outputted energies always have a van der Waals contribution that is on the order of 10^16.
This indicates you have a clash somewhere in your trajectory file. Use
the 'check' command in cpptraj or ptraj to see if there are any bad
overlaps.
> Also, the electrostatics calculated do not match those found by using imin=0 and the prmcrd file even though the coordinates in my trajectory are the same as those in the prmcrd file.
Are you certain that your input coordinates match those in your
trajectory? How did you generate the trajectory? Does your Amber
installation pass all tests (particularly the trajene, trajene_box,
and trajene_netcdf tests)?
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Aug 06 2013 - 15:30:03 PDT
