AMBER Archive (2008)

Subject: Re: AMBER: NAB conjgrad returns error?

From: Andreas Svrcek-Seiler (
Date: Thu Aug 07 2008 - 10:33:28 CDT

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

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

> readparm(m, ""); 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.

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

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