AMBER Archive (2006)

Subject: AMBER: ptraj warning while loading reference

From: Vlad Cojocaru (
Date: Mon Feb 27 2006 - 06:45:28 CST

Dear amber users,
    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. However my pdb file has definetely the same
number of atoms as the (mdcrd+top) files, which is 7661. It looks like
ptraj is also reading the REMARK and TER cards. However, the calculated
rmsd looks fine, the mask is properly recognized... so my question is
whether I am right that ptraj reads also REMARK and TER cards and if
yes, is this warning really necessary since anyway the atoms seem to be
read properly?

Best wishes


WARNING in ptrajProcessInputCoordinates(): Unexpected number of atoms
 encountered when reading PDB!
  loadPdb returned 7665
  getCoordinatesFromPdb returned 7661
  actual number of atoms is 7661

ptraj input:

trajin file.mdcrd
reference file-ref.pdb
rms reference mass out active-site-rmsd.dat :mask

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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