AMBER Archive (2006)

Subject: Re: AMBER: ptraj warning while loading reference

From: David A. Case (
Date: Mon Feb 27 2006 - 10:44:52 CST

On Mon, Feb 27, 2006, Vlad Cojocaru wrote:

> When calculating the rms of a trajectory to a reference structure in
> pdb format created by 'ambpdb -aatm' (see script below), I am always
> getting the warning below.
> WARNING in ptrajProcessInputCoordinates(): Unexpected number of atoms
> encountered when reading PDB!
> loadPdb returned 7665
> getCoordinatesFromPdb returned 7661
> actual number of atoms is 7661

This is a long-standing bug in ptraj. The best way to be sure that it is
innocuous is to remove all non-ATOM cards from the input pdb and see if you
still get the same results (without the warning).

..good luck...dac

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