Re: binary troubles

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Dec 05 2003 - 13:40:35 CST

Hello Michael,

You will need to have a non binary coord file with as well as the binary
forms. Don't know why, thats just the way it is...

an example
structure ./adjusted_wat.psf #file created from psfgen
coordinates ./adjusted_wat.pdb #ignored when bincoordinates is on
bincoordinates gwr_dyn_32ns_pme_on.restart.coor
binvelocities gwr_dyn_32ns_pme_on.restart.vel #used for restarting from
lastknown velocities

Brian

On Fri, 5 Dec 2003, Michael Grabe wrote:

> Dear NAMD,
>
> I am trying to use binary output files from my last run to restart my
> new run. I usually don't do this, I just use ASCII. But I get this error
> from NAMD2.5b1 when I try to restart:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Info: Configuration file is md.in
> TCL: Suspending until startup complete.
> FATAL ERROR: coordinates not found in the configuration file!
> Charm++ fatal error:
> FATAL ERROR: coordinates not found in the configuration file!
>
> Abort
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> I see that my binary coordinate file actually does exist in the current
> directory, and everything is specified correctly in the namd script
> (i think so at least). Is there a binary problem on the Mac OSX version?
> I didn't port my binary files between platforms.
>
> The relevant portion of the NAMD script is:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> # protocol params
> numsteps 100
>
> # initial config
> bincoordinates wt0_eq1.coor
> binvelocities wt0_eq1.vel
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
> If anyone has seen this problem, I would appreciate some advice,
> especially if I am forgetting something.
>
> Thanks,
> Michael
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> Post-doctoral Fellow
> Howard Hughes Medical Institute
> University of California, San Francisco
> 533 Parnassus Ave.
> San Francisco, CA 94143
> mgrabe_at_itsa.ucsf.edu
> tel: ++ 415.476.6585
> http://itsa.ucsf.edu/~mgrabe
>
>
>

-- 
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**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
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