Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ?

From: <>
Date: Sat, 1 Jan 2011 00:12:13 -0500 (EST)


wouldn't those just be the amino acid backbone parameters? You should find
them under

X -C -CA-X

etc. in the torsion section of the parm files. So there are no special
ones for different amino acids, only one set of backbone parameters AFAIK
(there are some angles specially for proline, at least in parm10.dat). But
those are not really *controlling* the cis/trans configuration in a
protein, your aar will stay cis or trans depending on their input
conformation during a normal simulation.

Kind Regards,


On Fri, December 31, 2010 12:32 pm, Jose Borreguero wrote:
> Dear amber users,
> I looked in parm94.dat to find the torsion potential controlling the cis
> or
> trans configuration of Proline, but I couldn't find it . Also, what is the
> analogous torsion potential for the other amino acids?

Dr. Thomas Steinbrecher
formerly of the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Dec 31 2010 - 21:30:02 PST
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