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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> >
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Received on Sat Jan 01 2011 - 07:30:02 PST
