From: Alan <>
Date: Wed, 17 Mar 2010 12:17:16 +0000

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.


On Wed, Mar 17, 2010 at 11:49, case <> wrote:

> On Wed, Mar 17, 2010, Peter Charles Kahuna wrote:
> >
> >
> >
> > 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

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
AMBER mailing list
Received on Wed Mar 17 2010 - 05:30:02 PDT
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