Dear Jason,
I had already tried this approach, building a bound GTP molecule from
the free GTP in that list. The problem is that the 3-phosphate part of
the molecule appears too stiff, hardly changing conformation in 10 ns. I
don't undertand if this is a real phenomenon or if there's something
wrong in the ff modifications.
Luca
On 04/27/12 17:12, Jason Swails wrote:
> Have you looked here at all?
> http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> They have a fairly extensive collection of parameters that can be used in
> Amber simulations.
>
> HTH,
> Jason
>
> On Fri, Apr 27, 2012 at 10:28 AM, luca codutti<luca.codutti.embl.de> wrote:
>
>> Dear Jacopo,
>> the second reference you pointed is on another subject, can you double
>> check it?
>>
>> J Mol Model.
>> <
>> http://www.ncbi.nlm.nih.gov/pubmed?term=Homeyer%20Essigke%20Meiselbach%20Ullmann%20Sticht#
>> 2007 Mar;13(3):431-44. Epub 2006 Dec 1.
>>
>>
>> Effect of HPr phosphorylation on structure, dynamics, and interactions
>> in the course of transcriptional control.
>>
>>
>>
>>
>> On 04/26/12 21:28, Jacopo Sgrignani wrote:
>>> J Phys Chem B. 2012 Feb 23;116(7):2259-68
>>
>> --
>> Luca Codutti, Ph.D.
>> Meyerhofstrasse 1, 69117
>> Heidelberg Germany
>> tel. +49(0)62213878965
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Luca Codutti, Ph.D.
Meyerhofstrasse 1, 69117
Heidelberg Germany
tel. +49(0)62213878965
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Received on Fri Apr 27 2012 - 08:30:03 PDT
