[gmx-developers] force field files for amber ff03* and ff99sb* for new release

[Shirts, Michael (mrs5pt)]

As long as they are contributed as additional force fields, not
modifications of the existing files -- reproducibility trumps anything else!

You might want to contact Eric Sorin, since he has done a lot of work in
implementing AMBER force fields in gromacs.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Robert Best <rbb24 at cam.ac.uk>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 5 Aug 2010 08:05:54 -0400
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] force field files for amber ff03* and ff99sb* for
> new release
> 
> 
> Since the Amber force fields will be part of the new release of gromacs
> (4.5), I'd like to suggest including the modifications which I've made
> (ff03-star, ff99sb-star). These have now been the subject of three
> publications (see below), and seem to offer significant improvements in
> folding proteins from different structural classes. Could you let me know
> whether/how I can contribute these?
> 
> Regards
> 
> Robert Best
> 
> 
> 
> @ARTICLE{best-2009-2,
>    author = "Robert B. Best and Gerhard Hummer",
>    title = "Optimized molecular dynamics force fields applied
>   to the helix-coil transition of polypeptides",
>    journal = "J. Phys. Chem. B",
>    volume = 113,
>    pages = "9004-9015",
>    year = 2009 }
> 
> @ARTICLE{best-2010-2,
>    author = "Robert B. Best and Jeetain Mittal",
>    title = "{Balance between $\alpha$ and $\beta$ structures in
> \textit{ab initio}
> protein folding}",
>    journal = "J. Phys. Chem. B",
>    volume = 114,
>    pages = "8790-8798",
>    year = 2010 }
> 
> @ARTICLE{mittal-2010-2,
>    author = "Jeetain Mittal and Robert B. Best",
>    title = "Tackling force field bias in protein folding simulations:
> folding of {Villin
>   HP35 and Pin WW} domains in explicit water",
>    journal = "Biophys. J.",
>    pages = "L26-L28",
>    volume = 99,
>    year = 2010 }
> 
> 
> 
> -- 
> Robert Best
> Royal Society University Research Fellow
> Department of Chemistry
> Lensfield Road, Cambridge CB2 1EW
> http://www.ch.cam.ac.uk/staff/rbb.html
> Tel: +44-(0)1223-336470 | Fax: +44-(0)1223-336362
> 
> 
> 
> -- 
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