AMBER Archive (2009)

Subject: Re: [AMBER] trajout problem

From: Sally Pias (sallypias_at_gmail.com)
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 

--
Sally Pias
Postdoctoral Fellow
Stony Brook University

On Mon, Nov 30, 2009 at 5:03 AM, Anna Reymer <reymer_at_chalmers.se> 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
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