AMBER Archive (2000)

Subject: Oct box and ptraj

From: Robert Matthew Fesinmeyer (rmf_at_u.washington.edu)
Date: Mon Aug 21 2000 - 13:12:50 CDT

This should be an easy question for someone to answer...

I have a protein in a truncated octahedron box of water. During the md
run, iwrap=0, so the coordinates are not written out as nice pretty 'box'.
When dealing with cubic systems, I've used ptraj to center my protein and
wrap the water back into a cube. In attempting to do this with the Oct, I
get my peptide centered in the pdb output, with what I guess is the Oct
box of water hanging off to one side. I'm certain I'm doing something
wrong. I looked through the documentation for ptraj and the tutorials,
but either the answer's not there, or I need to be beaten over the head
with it (quite probably the latter). Here's the ptraj input file I was
using:

trajin mdcrd
trajout mdcrd_wrapped
center :6
image
go

Thanks for your help.
Matt

_________________________
R. M. Fesinmeyer
rmf_at_u.washington.edu
Department of Chemistry
University of Washington