AMBER Archive (2006)

Subject: Re: AMBER: reading psf file

From: jojartb_at_pharm.u-szeged.hu
Date: Sat Nov 18 2006 - 02:38:26 CST

dear Tom,

thank you the quick response.i attached my psf file. this was genereted
with vmd1.8.5 using the built in tcl script.
the another file alanin.psf is a tutorial file. it is also attached.
the ptraj was yesterday compiled form Amber8. all bugfixes was allso apllied.
thank you for your help in advance!

Balazs Jojart

>
>> 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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