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

[Berk Hess]

Hi,

We have ported 7 Amber force fields into Gromacs.
Currently they are in the testing phase and available in the 4.5 beta
release
that can be downloaded from gromacs.org.

Adding force fields got much simpler now.
I guess that you just have a few modifications of existing Amber force
fields.
In that case you can take the existing force field files, make the changes,
document them in the forcefield.doc file and put them in a new directory.
pdb2gmx will then automatically read them.
You can upload them to the contributions page, but you might want to wait
with that until we have the first real 4.5 release.

We would have to look into the literature to see if it would be worth
adding them
to the standard distribution.

Berk

Shirts, Michael (mrs5pt) wrote:
> 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
>>
>>
>>
>> -- 
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
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>>     
>
>