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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Received on Sun Mar 05 2006 - 06:10:09 PST
