[AMBER] cpptraj/parmbox

From: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>
Date: Fri, 26 Sep 2014 00:13:59 -0700

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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Received on Fri Sep 26 2014 - 00:30:02 PDT
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