Problems witn parameter files!

From: Galina Petrova (ohgpp_at_chem.uni-sofia.bg)
Date: Mon May 10 2004 - 08:54:25 CDT

-----Original Message-----
From: "Galina Petrova" <GPetrova_at_chem.uni-sofia.bg>
To: namd-l_at_ks.uiuc.edu
Date: Mon, 10 May 2004 16:45:23 +0300
Subject: Problems witn parameter files!

Hi, everybody,

I would like to ask you something connected with the parameter files for
Charmm force field. First of all I could not understand some of the
abbreviations in the given files (for example N, NC2, NH1/2, 3/, NRH,
NR1/2, 3/, NY, CD, CPA, CPB, CPA, CPT, CT and many others in
par_all22_prot.inp or par_all27_prot.inp). Maybe the problem is that Iím
not a biochemist and donít work with protein structures. I try to
optimize simpler organic compounds. I guess that there is a nomenclature
for these abbreviations but I could find only some of them on the website
of Charmm and Amber.
Also I would like to know where I could find parameters not specified in
the parameter files given on the NAMD website. Could anybody tell me a
website or any articles containing such information?

Best wishes,
Galina Petrova

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