Re: [AMBER] how to measure atom distance in md trajectories using ptraj program

From: Jason Swails <>
Date: Wed, 28 Mar 2012 15:23:30 -0400

The AmberTools manual (distributed with AmberTools and also available on, describes how to use each feature of ptraj, so you should
consult the manual first. You should also look at the Amber mask syntax
and how to use it (the manual and the "ambmask" program will be helpful

If, after you've tried the suggestions in the manual (and the tutorials
are helpful as well), and you sill have problems, you should email the
list with specific details -- i.e., what exact commands did you try
(don't say what you tried or meant to do, but what you _actually_ did),
and what (exact) output did you receive.

If you suspect a bug (and I highly doubt the distance calculation
routine in ptraj has a bug), you should also include details about your
operating system and compilers.


On Wed, 2012-03-28 at 10:26 -0700, Bala Subramani wrote:
> im facing problem in measuring distance b/w met C=O and asn N-H in
> ptraj program... could anyone fix this problem... thanks in
> advance....
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 28 2012 - 12:30:04 PDT
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