[AMBER] Cpptraj to center molecules

From: Aseel Bala <balaahme.msu.edu>
Date: Fri, 11 Aug 2017 15:36:06 -0400

Hello everyone,


I am using Amber to center a cluster of hydrogen bonded alcohol molecules in
a frame.

Say molecules number 4 and 5 are hydrogen bonded to one another (and I have
verified this by looking at O-O distances and O-H-O angles and made sure
they match my criteria).


I am currently using the following syntax with cpptraj to center the
molecules 4 and 5 in the frame:


parm ../../../simbox.prmtop

trajin ../../1801.inpcrd

center :4,5 origin

image origin center familiar

trajout c4_5.pdb pdb




This works fine if the two molecules are near each other in a given frame.


However, I am running into an issue when 4 is on one edge of the frame and 5
is on the other edge. In these situations, 4 is actually H-bonded to an
'image' of 5 produced by the periodic boundary condition. Let's call this
image 5prime.


In this case, cpptraj actually centers 4 and 5 instead of 4 and 5prime.


Is there a way that cpptraj can be used to center a molecule and the closest
image of another molecule to it? So that I would be able to have 4 and
5prime in the center?


Thank you very much in advance!


Aseel M. Bala 
Michigan State University
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Received on Fri Aug 11 2017 - 13:00:02 PDT
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