Re: AMBER: convert_trajectory

From: Thomas E. Cheatham, III <>
Date: Wed, 27 Jul 2005 15:27:57 -0600 (Mountain Daylight Time)

> I try to use ptraj in AMBER8 to ransfer NAMD trajectory to AMBER trajectory.
> But some errors occur when PSF is read like:
> Error scanning a value: parm->NBONH
> Error scanning a value: parm->NBONA

ptraj is not recognizing the PSF file format; the program expects the
first line of the PSF file to be "PSF" or "PSF ". If the top of your
PSF file does not look like this, ptraj will not recognize it and will
assume it is an AMBER prmtop.

> Another question: when ptraj outputs AMBER trajectory from NAMD trajectory,
> do orders of atoms fit to AMBER topology?

No. There must be an exact 1-1 mapping in the atom order between the PSF
and the AMBER topology as there is no easy/general way to do the mapping
or reordering of atoms on the fly (particularly as there is no guarantee
or requirement that the atom names are equivalent between the PSF and
AMBER topology since we only parse one of these files and do not check the
results; to do this would require reading both topology formats initially
and setting up the mapping which would be quick tricky, could be done, but
is not at present implemented/done). When you build the corresponding
AMBER topology, you must make sure that the atoms and residues are in
exactly the same order otherwise the resulting trajectory will be


  Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
  Depts of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
  Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
  University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112

 (801) 587-9652; FAX: (801) 585-9119
       BPRP295A / INSCC 418

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Received on Wed Jul 27 2005 - 22:53:00 PDT
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