[gmx-developers] Short question: Preferred FF for proteins

["Pablo García Risueño"]

Thank you very much to all for your interesting explanations.

Best regards


> Perhaps this thread should be moved to the user list.
>
> Your question very much depends on the problem that you want to study.
> While I prefer the Amber99sb-ILDN ff for most simulations, the Charmm
> forcefield often has superior support for lipids and carbohydrates,
> which can be vital components of a "protein" simulation.
>
> Grant.
>
>
>
> On Mon, Aug 12, 2013 at 7:15 AM, Erik Lindahl
> <erik.lindahl at scilifelab.se> wrote:
>> Hi,
>>
>> I would very much agree with Michael, and it's my own FF of choice, but
>> on the other hand: If anybody showed me a result they could only get
>> with Amber99sb-ILDN but no other force field, I wouldn't trust it!
>>
>> Cheers,
>>
>> Erik
>>
>> On Aug 12, 2013, at 2:12 PM, "Shirts, Michael (mrs5pt)"
>> <mrs5pt at eservices.virginia.edu> wrote:
>>
>>> Not really a gromacs developer question, more of a user question.
>>>
>>> amber99sb-ildn is probably the force field that has been most heavily
>>> validated for proteins.  Check some of the Shaw group papers.
>>>
>>> That's not to say that others might not be sufficient, just that more
>>> CPU-hours have been burned studying that force field than any other,
>>> and the
>>> results have not been bad.
>>>
>>>
>>> Best,
>>> ~~~~~~~~~~~~
>>> Michael Shirts
>>> Assistant Professor
>>> Department of Chemical Engineering
>>> University of Virginia
>>> michael.shirts at virginia.edu
>>> (434)-243-1821
>>>
>>>
>>>> From: Pablo García Risueño <Risueno at physik.hu-berlin.de>
>>>> Reply-To: Discussion list for GROMACS development
>>>> <gmx-developers at gromacs.org>
>>>> Date: Mon, 12 Aug 2013 14:06:41 +0200
>>>> To: <gmx-developers at gromacs.org>
>>>> Subject: [gmx-developers] Short question: Preferred FF for proteins
>>>>
>>>> Dear developpers
>>>>
>>>> We would like to ask for your expert knowledge to notice which is the
>>>> Force Field (or FF family) which is customarily preferred for
>>>> simulations
>>>> of peptides and proteins.
>>>>
>>>> Thank you very much. Best regards
>>>>
>>>>
>>>> --
>>>>
>>>> Dr. Pablo García Risueño
>>>>
>>>> Institut für Physik und IRIS Adlershof, Humboldt Universität zu
>>>> Berlin,
>>>> Zum Grossen Windkanal 6, 12489 Berlin, Germany
>>>>
>>>> Tel. +49 030 209366369
>>>>
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>>>
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--

Dr. Pablo García Risueño

Institut für Physik und IRIS Adlershof, Humboldt Universität zu Berlin,
Zum Grossen Windkanal 6, 12489 Berlin, Germany

Tel. +49 030 209366369