AMBER Archive (2008)

Subject: Re: AMBER: GAFF for organic crystals

From: Junmei Wang (junmwang_at_gmail.com)
Date: Mon Jun 23 2008 - 10:16:50 CDT

Hi, Jeremy,
According to paper J Comput Chem 25: 1157–1174, 2004, the average rmsd
atomic displacements of 74 crystal structures of small molecules is 0.26
angstroms. So the rmsd of 4,4'-bipyridine is a little bit larger. However,
if you minimize the MD structures first, you may get smaller RMSD.

Gaff and amber use the same functional form and no specific term is included
to account for coplanar interactions

Best

Junmei

On Fri, Jun 20, 2008 at 3:05 AM, Rabone, Jeremy <
Jeremy.Rabone_at_liverpool.ac.uk> wrote:

>
> Hello all,
>
> I have just started a project to investigate porous organic framworks,
> for which I intend to use the AMBER GAFF force-field. I'm actually using the
> force-field in a different simulation program (DL_POLY), using the
> parameters taken from prmtop files prepared using antechamber and leap. At
> the moment I am looking at small simulations 4,4'-bipyridine and an
> Ni-aspartate to see how closely the simulations match experiment (and if I
> have transferred the force-field correctly!). The RMSD atomic displacements
> for averaged trajectories I get are 0.585 A for bipyridine and 0.419 A for
> Ni-aspartate at 273K atmospheric pressure. Do these values match the sort of
> RMSD seen by other GAFF users in simulations of organic crystals ?
>
> In the bipyridine one of the rings seems to buckle away from a ring in an
> adjacent molecule rather more than is found in experiment. It looks like a
> interaction which would favor co-planarity of aromatic rings would
> counteract this; is there an such an intermolecular force which stabilises
> co-planarity between aromatic rings and which the GAFF does not include ?
>
> Thanks for any comments,
>
> Jeremy
>

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