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
> >
> >
> > _______________________________________________
> > 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)
> _______________________________________________
> 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
Received on Wed Mar 17 2010 - 05:30:03 PDT
