AMBER Archive (2002)

Subject: RE: How to check whether the trajectory file matches the coordinates file or not?

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Mon Sep 09 2002 - 14:32:27 CDT

>> After 100ps MD, I plan to look at the generated structure in Moil-View.
>> And I stripped out the water from coordinates file (restrt) and
>> trajectory file (trajetory) using ptraj, and from topology file (prmtop)
>> using rdparm. Then in the Moil-View, the structure looked crazy when
>> viewd trajectory. It seemed the trajectory file doesn't match the
>> coordinates file (restrt) or topology file (prmtop).

It's possible that when you strip out the waters, you may also need to specify
"nobox" in your trajout line. I experienced a similar problem to what you
describe where the first frame of my trajectory output from ptraj looked fine,
but subsequent frames were "crazy." Turns out the coordinates were being
offset by one for each frame because of box coordinates I didn't have! (Check
comment in ptraj manual in trajout section in reference to keyword nobox.)

Good luck!

Kristina

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu