[AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain

From: Ԫ <tangyuanhui08.126.com>
Date: Wed, 6 Jun 2018 00:53:49 +0800 (CST)

Hello all,


This is Yuanhui. I want to calculate the distance between two residues as :i and :j, and i, j can be changed during a loop. However, the distance mask doesn't recognize the word :i. The input file is written like this:


parm *.prmtop
trajin md15.mdcrd 1 last 200
i=2
j=3
distance dist :i :j out dist.dat


Is there a way can make the cpptraj recognize the variable 'i' and 'j', because I want to change their values.
Best wishes!



--
Dr. Yuanhui Tang
Ralph E. Martin Department of Chemical Engineering
University of Arkansas
Cato Springs Research Center
Fayetteville, AR 72701
email: yt006.uark.edu
voice: (479) 409-9989
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Received on Tue Jun 05 2018 - 10:00:02 PDT
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