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

From: Thomas Cheatham <>
Date: Fri, 17 Jun 2011 12:30:09 -0600 (Mountain Daylight Time)

> 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.


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Received on Fri Jun 17 2011 - 12:00:03 PDT
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