AMBER Archive (2009)

Subject: Re: [AMBER] trajout problem

From: Sally Pias (
Date: Mon Nov 30 2009 - 13:01:52 CST

I have had trouble reading restart files into ptraj before. In my
case, I was able to get around the problem by using ambpdb to convert
the restart files to pdb format. Then, ptraj read them successfully.
I don't know if this could be a small ptraj bug that has been
overlooked? (I was using ptraj from Amber 9.) In my case, I was
trying to use the restart files as reference coordinates for RMSD
calculations. Unfortunately, I don't have the actual ptraj scripts
used. The restart files were produced by sander and were functional
in that I could successfully restart a trajectory from them.

Anna, can you provide the ptraj script that is giving the error?


Sally Pias
Postdoctoral Fellow
Stony Brook University

On Mon, Nov 30, 2009 at 5:03 AM, Anna Reymer <> wrote: > 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. > > Regards, > Anna > > ----------- > Anna Reymer, PhD student > Physical Chemistry, > Department of Chemical and Biological Engineering > Chalmers University of Technology > Kemivägen 10 > SE-412 96 Gothenburg > Sweden > > Phone: +46-(0)31-7722815 > _______________________________________________ > AMBER mailing list > > >

_______________________________________________ AMBER mailing list