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
go
quit
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
