Re: [AMBER] cpptraj/parmbox

From: Jason Swails <>
Date: Fri, 26 Sep 2014 09:47:45 -0400

On Fri, 2014-09-26 at 00:13 -0700, amirhossein taghavi wrote:
> Hello everyone,
> My rpoblem is not directly related to MD but as I use Amber cpptraj to
> analyze my data, I wondered may some one could have some help!!
> I have a CG model of DNA in xyz format and I am using cpptraj to do
> some measurements on bonds,angles and dihedrals.The problem is, for
> example, when I calculate the base interdistances with piece of a
> script I have, in some frames the distance is calculated with the
> image of particle at the end of the box, like say my box is 136A. so
> if the usual BB distance is between 5-7A is some frames it jumps tp
> 136.
> I have added parmbox information to the script but the problem still
> exists.
> any help or suggestion is highly appreciated.

By default, cpptraj uses the minimum image convention when computing
distances (unless you use the keyword "noimage"). If you are getting
wonky distances, perhaps your box is not correctly defined?

Your cpptraj output should provide information about your files (like,
for instance, any box information that may be present). Does it look
right to you?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Sep 26 2014 - 07:00:02 PDT
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