AMBER Archive (2002)

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

From: Ling Zhang (lz267_at_nyu.edu)
Date: Mon Sep 09 2002 - 13:31:13 CDT

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