Re: AMBER: convert_trajectory

From: Wei Chen <>
Date: Wed, 27 Jul 2005 19:07:55 -0400


Thanks a lot!

I change a little bit to make PSF recognized. But ptraj dumps
one more residue at the beginning of AA sequences. Actually,
it duplicates the first residue. Why does this happen?

Wei Chen

"Thomas E. Cheatham, III" <>:

> > 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
> meaningless.
> --tom
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Jul 28 2005 - 00:53:01 PDT
Custom Search