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

[Grant Rotskoff]

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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