AMBER Archive (2008)

Subject: RE: AMBER: Trajectory in "Sietraj"

From: Purisima, Enrico (
Date: Tue Jun 03 2008 - 08:55:20 CDT

Dear Alfredo,

The trajectory used is an Amber trajectory with water molecules stripped out and generated with the nobox option. The suffix .trj was an arbitrarily chosen suffix in the examples and not meant to imply Gromacs files. Could you post the error messages? A common cause of errors is missing atom types.

Enrico O. Purisima
Biotechnology Research Institute
National Research Council Canada

-----Original Message-----
From: [] On Behalf Of Alfredo Quevedo
Sent: Tuesday, June 03, 2008 9:35 AM
Subject: AMBER: Trajectory in "Sietraj"

Dear Amber users. I have recently seen the link of the "Sietraj" application in Amberīs homepage, and found it ver interesting. I downloaded it and run the examples with everything running ok. I tried to apply this package to analyze my trajectories generated with Amber8 and found some errors with the calculation stoped. Searching the source of the problem, I find out that the examples of Sietraj are based on a .trj trajectory (I think that is Gromacs), so here comes my question: Has anyone tryed this software using an Amber trajectory? Otherwise, is there a way to convert the .mdcrd files into a .trj file?
Thanks in advance for the help,
Best regards

Alfredo Quevedo
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