I had not thought of that, Thanks!
-Jose
On Sat, Jan 1, 2011 at 10:02 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> that's not really correct, since the dihedral parameters are only one
> factor
> controlling the energy. the 1-4 nonbonded interactions certainly differ for
> proline.
>
>
> On Sat, Jan 1, 2011 at 9:56 AM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > 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 - 09:00:04 PST
