Re: [AMBER] Fwd: warning in ptraj check coordinates()

From: Sajeewa Pemasinghe <>
Date: Fri, 17 Jun 2011 14:53:09 -0400

Thank you very much. That cleared lot of doubts.

On Fri, Jun 17, 2011 at 2:30 PM, Thomas Cheatham <> wrote:

> > WARNING in checkCoordinates(): The actual number of atoms (99999)
> > does not match the expected number of atoms (167571) in (k1_wat.pdb)
> > With this version of the code, this will likely lead to program
> failure!!
> This occurs when the PDB does not match the prmtop and is supported to
> allow you to load a truncated PDB file as a reference file (i.e. only the
> protein). As long as there is a 1-1 match (in order from atom 1->N), and
> no more than N atoms are used in the match, things should be OK. The
> warning is just that, a warning to alert you that your PDB does not have
> the same number of atoms as the prmtop expects.
> My guess is that the PDB format has overflowed in your case since it says
> 99999 atoms which is one less than can fit in the formatted field so
> essentially many of the waters (the likely atoms after 99999) are not in
> fact loaded up.
> --tec3
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Received on Fri Jun 17 2011 - 12:00:04 PDT
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