[AMBER] Translate command with ptraj

From: Logan Ahlstrom <logana.email.arizona.edu>
Date: Fri, 10 Dec 2010 18:21:24 -0700

 I have run a simulation of six protein chains with non-orthogonal boundary
conditions. Now I want to extract specific chains (i.e two of them at a
time) from the trajectory in order to analyze interactions between them.
Below is the script I am using in order to extract residues 1-66 (chain 1)
and 199-264 (chain 2) and then to translate chain 2 in the -Y direction.
(Each chain is identical and is 66 residues long).

 trajin ../../../traj/PSQ_xtal/test.mdcrd 1 100 1

box x 50.524 y 50.524 z 48.148 alpha 90.0 beta 90.0 gamma 120.0 fixx fixy
fixz fixalpha fixbeta fixgamma

strip :265-396

strip :67-198

center :1-132 mass origin

translate :67-132 x 0 y -50.524 z 0

trajout ../../../traj/PSQ_xtal/interface6/test.out.mdcrd nobox

 In the outputted two-chain trajectory, the second chain is translated in
the correct direction but it does not show the same interface as in the
original trajectory. Perhaps ptraj is treating gamma as 90.0 instead of
120.0 degrees, even though I am explicitly giving the program the box
lengths and angles? I have tried input trajectories with/without periodic
boundaries specified, as well. Any suggestions/input would be much


Logan S. Ahlstrom
Ph.D. Candidate
Department of Chemistry and Biochemistry
University of Arizona
AMBER mailing list
Received on Fri Dec 10 2010 - 17:30:02 PST
Custom Search