thanks for your suggestions. Setting maxcyc to 10 and ntpr=1 didnt change anything. However, when I tried running sander instead of pmemd it worked fine (!!), no errors given and everything looks ok..
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 07 June 2013 21:01
To: AMBER Mailing List
Subject: Re: [AMBER] unable to run minimizations after new installation of amber11
On Fri, Jun 07, 2013, Amparo Garcia Lopez wrote:
>
> /usr/local/amber11/bin/pmemd -O -i min1.in -o TSL2_1N8R.wat.min1.out -inf TSL2_1N8R.inf -c TSL2_1N8R.wat.crd -ref TSL2_1N8R.wat.crd -r TSL2_1N8R.wat.min1 -p TSL2_1N8R.wat.top -x TSL2_1N8R.wat.min1.x -e TSL2_1N8R.wat.min1.ene
If the TSL2_1N8R.wat.min1 file created here is empty, you need to find out
why--i.e. everything else beyond this will fail, as you point out in your
email. If the TSL2_1N8R.wat.min1.out is indeed uninformative, set maxcyc to
10 and ntpr=1 and try to get more information. If that doesn't work, try
running sander instead of pmemd...sometimes with odd errors one program or the
other can give better error reporting.
...good luck...dac
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Received on Sat Jun 08 2013 - 09:30:02 PDT
