AMBER Archive (2009)

Subject: [AMBER] Nonstandard molecules simulated with parm99EP ?

From: Marek Maly (
Date: Mon Jun 29 2009 - 12:06:27 CDT

Dear Amber users,
recently I have read a very interesting article:

( free download at (section PUBLICATIONS) )

related to simulations of Naphthyridine-based dendrimers using Amber7
and parm99EP forcefield. The authors have obtained an excellent agreement
experimental binding energy results regarding to complexation with small
at dendrimer core in explicit solvent (10% CH3-CN and 90% CHCl3).
I was a little bit surprised since I thought that parm99EP forcefield
is devoted mainly to simulations of nucleid acids and proteins and for
of such "exotic" molecules like for example above mentioned class of
GAFF is more suitable.

Unfortunately the authors didn't mention some important details - for
example how they
parametrised their dendrimers for Amber calculations in particular how
they succeeded
to create relevant PREPIN files using parm99EP forcefield.

So I have just the simple technical question: How it is possible to force
the antechamber
to use some different forcefield from GAFF ( like for example parm99EP )
for parametrisation of the
relevant residui (generating of PREPIN/FRCMOD files) ?

Does anybody have positive experiences with usage of parm99/parm99EP for
simulations of some non-nucleic/non-protein
molecules or did someone even try to compare GAFF results with
parm99/parm99EP ones regarding to simulation of "nonstandard" molecules ?
(By term "nonstandard" I mean here non-protein, non-nucleic acid)

Thanks in advance for your feedback.



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