[AMBER] Using iwrap with a dimer

From: Caitlin Scott <cescott.caltech.edu>
Date: Thu, 21 Aug 2014 06:45:28 -0700 (PDT)

Hi Everyone,

I'm trying to run a NPT simulation of a dimer. There are two chains, each
with residues numbered 1-93. When I set iwrap=1 and try to visualize the
simulation in vmd, the two protein chains are separated and put into
different corners of the waterbox. I'm trying to use cpptraj to put the
dimer into the center of the waterbox with the following input file:

trajin 01_Prod.cdf
unwrap :1-2880 byatom
center :1-2880 origin
image origin center familiar
trajout out.cdf cdf nobox

This doesn't fix the problem--the two protein chains are still separated.
Can someone please tell me what's wrong with the above *.in file or offer
a suggestion on how to fix this issue?


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Received on Thu Aug 21 2014 - 07:00:02 PDT
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