Re: [AMBER] cpptraj/parmbox

From: Daniel Roe <>
Date: Fri, 26 Sep 2014 07:59:59 -0600


We need much more information on how the original trajectory was
generated, as well as the full cpptraj output to even begin to
diagnose this problem.


On Fri, Sep 26, 2014 at 1:13 AM, 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.
> Thanks in Forward
> _______________________________________________
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Sep 26 2014 - 07:30:02 PDT
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