AMBER Archive (2006)

Subject: Re: AMBER: reading psf file

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Nov 17 2006 - 18:28:45 CST

> i would like to analyze my namd job with amber ptraj. is able ptraj to
> read in the psf file? becuase i obtained the following erros:

What version of ptraj? I routinely process CHARMM PSF and DCD files,
however I haven't played with all variants so there could be a problem.

> Amber8 Module: ptraj
>
> Input the name of an AMBER prmtop or CHARMM PSF: 128_dspc_wat.psf

What ptraj looks for is "PSF " or "PSF" at the top of the file; if this is
not the case, how did you generate the PSF or did the PSF format change?

>
> with an another psf file (from vmd, alanin.psf):
>
> REMARKS FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PSF"
> REMARKS PARAM11.PRO ( from PARAM6A )
> REMARKS ===========

I have not seen "REMARKS" at the top of PSF files previously. Are you
sure this is a PSF and not a MD output or some such? You can send me a
copy of the first PSF and I can try to decipher...

--tom

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham
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