AMBER Archive (2002)

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

From: Shixiang Yan (sy8_at_SCIRES.ACF.NYU.EDU)
Date: Mon Sep 09 2002 - 13:53:04 CDT

you can use ptraj to transform one frame of your trajectory into pdb file.
then check the correctness of your file. good luck... yan

On Mon, 9 Sep 2002, Ling Zhang wrote:

> Dear all:
>
> 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). But how can I check
> it? Is there a way to transfer trajectory file into a PDB file or some
> other format? Thanks a lot.
>
> Best,
> Ling
>