Many thanks, Thomas. I had thought the torsion potential for Proline would
have a lower barrier than that of a different amino acid for parm94 or
parm98.
If that's the case, then an umbrella sampling of the trans-to-cis
isomerization of proline will render a free energy profile no different than
if I choose another amino acid.
-Jose Borreguero
On Sat, Jan 1, 2011 at 12:12 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> 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,
>
> Thomas
>
> 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 Sat Jan 01 2011 - 07:00:02 PST
