Re: [AMBER] PairwiseDistance file location

From: Daniel Roe <>
Date: Thu, 4 Oct 2012 08:35:35 -0600


On Thu, Oct 4, 2012 at 2:28 AM, vaibhav dixit <> wrote:
> Is there any flag in the cluster command to specify this file, I can't see
> it in the AmberTools, Amber manual.

As far as I know the file name is hard-coded to PairwiseDistances. Why
not just soft-link the file to the directory you intend to run
clustering, e.g.:

cd <target directory>
ln -s <source-pairwise-distance-location> .

> Can I run all the jobs from one ptraj input file, if so how? I tried this:

Yes you should be able to. Are you sure you aren't getting any errors?
Are you able to run the commands separately?


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Oct 04 2012 - 08:00:03 PDT
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