Re: [AMBER] RDPARM

From: Philippe Pinard <pp_amber17.yahoo.com>
Date: Wed, 4 Aug 2010 17:24:56 -0700 (PDT)

How do I use parmchk from AmberTools 1.0?
/opt/software/SGI/AMBER/amberTools-1.2/src/antechamber



________________________________
From: case <case.biomaps.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wed, August 4, 2010 10:48:36 PM
Subject: Re: [AMBER] RDPARM

On Wed, Aug 04, 2010, Philippe Pinard wrote:

> Addding "-a Y" works for me. What version of parmchk (e.g. version of
> AmberTools or Amber are you using?

> This is release 1.0 of AmberTools.
> amber9.

Looking at the logs, it looks like there was a bug with this flag that was
corrected in Feb., 2008. It should be correct in AmberTools 1.0, but not
in amber9.

You email message mentioned $AMBERHOME/exe/parmchk, which makes me think you
might be using the amber9 version, not the one from AmberTools. In any event,
upgrading to the current codes is probably a good idea, but you might get away
with just running the AmberTools v1.0 program.

....dac


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Received on Wed Aug 04 2010 - 17:30:03 PDT
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