I believe you should see Amber 10 manual, page 189:
6.7.3. Chirality restraints: makeCHIR_RST
Usage: makeCHIR_RST <pdb-file> <output-constraint-file>
We also find it useful to add chirality constraints and trans-peptide ω
constraints (where appro- priate) to prevent chirality inversions or peptide
bond flips during the high-temperature portions of simulated annealing runs.
The program makeCHIR_RST will create these constraints. Note that you may
have to edit the output of this program to change trans peptide constraints
to cis, as appropriate.
Alan
On Wed, Apr 14, 2010 at 13:44, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> I believe this type of thing would be accounted for by an improper
> dihedral term. If there is no improper dihedral term for this group,
> you may have to create one via an frcmod to your molecule. I do not
> believe this is done by default, though it's easy to check in gaff.dat
> or your existing frcmod if you created one.
>
> The path I'd tentatively suggest is to get the energy profile of
> chiral inversion by using restraints and minimization via sander on
> some type of model system with that group and then fitting an improper
> term to adjust that profile to your target (maybe generated by a
> quantum calculation...)
>
> Of course others may chime in with better ideas, this is just the one
> that popped to mind.
>
> Good luck!
> Jason
>
> On Wed, Apr 14, 2010 at 3:43 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> > Dear Amber community!
> >
> > Amines of the type NHRR' are chiral because of the lone pair of
> electrons.
> > The energy barrier for inversion of stereocenter is about 7 klcal/mol.
> > I wonder if there is some mechanism in GAFF to prevent the amine
> > inversion. I suppose that 7 klcal/mol barrier crossing is a
> low-probability
> > event on the time scale of MD simulations, nevertheless I've observed
> > inversion of my amine during equilibration stage.
> >
> > Thanks in advance!
> > --
> > Dmitry Nilov,
> > Lomonosov Moscow State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed Apr 14 2010 - 06:30:04 PDT
