AMBER Archive (2008)

Subject: RE: AMBER: NAB conjgrad returns error?

From: Carra, Claudio (JSC-SK)[USRA] (claudio.carra-1_at_nasa.gov)
Date: Thu Aug 07 2008 - 11:19:52 CDT

Hi Andreas,
thanks a lot for your prompt answer,

> I got the following problem by trying to run an optimization with NAB.
> I'm interested in the parallel version of nmode, but somehow I cannot
> manage to reach the end of the optimization.

...does the same error occur when you use the serial version (no openmp
or
mpi)?

          I guess I'm only using the serial at the moment.

...which version are you running (the latest being distributed with
Amber
Tools 1.2)?

        yes, 1.2 with the latest patch updates.

> -------
> molecule m;
> float x[573], fret, ier;
>
> m = getpdb_prm( "snapshot_lig.pdb.3", "leaprc", "", 0 );
...here you are reading in a pdb file and generate a prmtop-structure

> readparm(m, "6ssDNA.top");
...here you read in a prmtop-structure for your molecule,
most probably just overwriting the prmtop structure you have generated
in
the line above. This doesn't seem to be related to your problem,
but shouldn't be done anyway.

        ok, that was just one of the trial test I did, but I got
        the error either way. But thanks for the tip!
        

...If you could mail me all the input files, I'd be happy to take a
deeper
look.

        they are attached
        thanks a lot
        sincerely
        claudio



  • application/octet-stream attachment: run.nab

  • application/octet-stream attachment: leaprc
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