Is that in the manuals? Sorry, if so, would you mind to point me out? I am
doing a review for an article I am writing and that would be interesting to
know more.
Many thanks,
Alan
On Wed, Mar 17, 2010 at 12:26, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it is definitely possible to use chirality restraints using the Amber
> "proper" dihedrals. we do this routinely. there is even a utility included
> in Amber to set it up.
>
>
>
> On Wed, Mar 17, 2010 at 8:17 AM, Alan <alanwilter.gmail.com> wrote:
>
> > Hello Case,
> >
> > Apologises if it sounds I am hijacking this topic.
> >
> > I heard once, from personal communication, about using AMBER FF in CNS,
> > years ago, for solving X and NMR structures but they were facing a
> problem
> > about inverting chirality (residues were ending up in D enatiomer form
> > instead of L) during simulated annealing and in the end they concluded it
> > was because of AMBER FF "lacking" improper dihedrals in the way like
> > CHARMM,
> > GROMOS, Engh/Huber and others does.
> >
> > Since I was not there when they did those tests and we never discussed
> > further on this topic (is all in their memories apparently, no paper
> > published), I am wondering if what they experienced seems probably
> correct.
> >
> > I know this paper
> >
> > B. Xia, V. Tsui, D.A. Case, H.J. Dyson, and P.E. Wright. "Comparison of
> > protein solution structures refined by molecular dynamics simulation in
> > vacuum, with a generalized Born model, and with explicit water". J.
> Biomol.
> > NMR 22, 317-331 (2002).
> >
> > However is only on water refinement.
> >
> > Many thanks in advance.
> >
> > Alan
> >
> > On Wed, Mar 17, 2010 at 11:49, case <case.biomaps.rutgers.edu> wrote:
> >
> > > On Wed, Mar 17, 2010, Peter Charles Kahuna wrote:
> > > >
> > > > http://ambermd.org/
> > > >
> > > > I would like to know how the improper contributions are included?
> > > >
> > > > i.e. what is the form of the function?. Is it simmilar for example to
> > > > the CHARMM forcefield?
> > >
> > > Improper terms in Amber have the same functional forms as "proper"
> > > dihedrals.
> > > This is different from CHARMM.
> > >
> > > ...good luck....dac
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Alan Wilter Sousa da Silva, D.Sc.
> > PDBe group, PiMS project http://www.pims-lims.org/
> > EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
> > +44 (0)1223 492 583 (office)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Thu Mar 18 2010 - 08:30:03 PDT
