AMBER Archive (2008)

Subject: AMBER: GAFF for organic crystals

From: Rabone, Jeremy (
Date: Fri Jun 20 2008 - 03:05:18 CDT

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,


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