Re: [AMBER] Distance calculations with ptraj

From: Daniel Roe <>
Date: Mon, 8 Oct 2012 16:07:15 -0600

On Mon, Oct 8, 2012 at 2:18 PM, Kira Armacost
<> wrote:
> I only used the .binpos file to check to see if it would work. I originally used the .crd file generated from the trajectory including box information. My hydrogen bond calculations worked with imaging using the .crd file so I know that's not the problem.

Do you mean you ran the 'image' command with the 'hbond' command?
Right now I believe imaging inside the hbond command is disabled, so
by itself the hbond command would work whether the box info is there
or not.

If you would like to send me (off-list) the topology file and one or
two frames of the trajectory in question I can look into this further.


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 Mon Oct 08 2012 - 15:30:04 PDT
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