AMBER Archive (2006)

Subject: Re: AMBER: ptraj warning while loading reference

From: Vlad Cojocaru (
Date: Mon Feb 27 2006 - 11:00:43 CST

Dear David,

I have checked that some times and it does give the same results so it
really looks innocuous.. However, its a bit painful to do the checking
all the time because I have long scripts that automatically go through a
series of analysis steps... In some of them I need the TER cards to be
there ...

So I guess one can live with the warning if its known to be harmless ...
and so far it does seem harmless ...


David A. Case wrote:

>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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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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