AMBER Archive (2009)

Subject: [AMBER] trajout problem

From: Anna Reymer (
Date: Mon Nov 30 2009 - 06:03:38 CST

Dear All,
I have the following problem.
When I try to run MD where I use my complex.rst as an input coordinates file and Sander produces no output files, neither trajectory file, nor restart file and the out file is just empty.

I have tested the input and topology files and they are fine, and the problem seems to be in the restart file.

I produce the restart file from a trajectory file, using ptraj script:

trajin md_2_complex.mdcrd 4243 4243
trajout complex.rst restart nobox append

I guess the problem is in initial rst file, which, for some strange reason, contains just columns of zeroes in the second half.

Has anybody any advice? Thanks in advance.


Anna Reymer, PhD student
Physical Chemistry,
Department of Chemical and Biological Engineering
Chalmers University of Technology
Kemivägen 10
SE-412 96 Gothenburg

Phone: +46-(0)31-7722815
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