Marek,
If you read the paper describing parm99, it is explained that this FF
was a first attempt in the direction of organic structures.
If you look in R.E.DD.B. the project of C. Cezard
Bulky Alcohols
http://q4md-forcefieldtools.org/REDDB/projects/W-79/
Author(s) Christine Cézard, Corey A. Rice and Martin A. Suhm
Journal of Physical Chemistry A
Year 2006 Volume 110 Page(s) 9839 - 9848
The authors describe in their paper that parm99 was better than GAFF
for what they wanted to study...
regards, Francois
> Dear Amber users,
> recently I have read a very interesting article:
>
> http://pubs.acs.org/doi/abs/10.1021/ma062610a
>
> ( free download at http://www.mose.units.it (section PUBLICATIONS) )
>
> related to simulations of Naphthyridine-based dendrimers using Amber7
> and parm99EP forcefield. The authors have obtained an excellent
> agreement with
> experimental binding energy results regarding to complexation with
> small ligands
> 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
> simulations
> of such "exotic" molecules like for example above mentioned class of
> dendrimers, 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.
>
> Best,
>
> Marek
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Received on Mon Jul 06 2009 - 12:14:46 PDT
