Thanks a lot Francois,
Maybe I am blind here but I could not find GDP in the project F-90 or
F-91 .. I also tried to search the RED database with "GDP" or "GTP" as
molecule names but no results matched.
Could you please point me more precisely how to efficiently search for GDP ?
Thanks a lot
Vlad
P.S. Do you know any reference that used these parameters ?
On 08/28/2012 12:15 PM, FyD wrote:
> Vlad,
>
> You might look in R.E.DD.B.; See the F-90 & F-91 projects:
> http://q4md-forcefieldtools.org/REDDB/Projects/F-90/
> http://q4md-forcefieldtools.org/REDDB/Projects/F-90/script1.ff
> http://q4md-forcefieldtools.org/REDDB/Projects/F-90/script3.ff
>
> You will find many FF libraries for more than 200 cofactors; GMP, GDP,
> GTP are obviously available...
>
> regards, Francois
>
>
>
>
>> I am looking into starting simulations of a protein that has a GDP and a
>> MG ion in the active site.
>> I know that in the database of AMBER parameters there are the Carlson
>> parameters for GDP and the new Sorensen parameters for MG.
>>
>> I also found this comment from David Case which made me wonder about
>> GDP. Is there anything new on the paper mentioned there ?
>> http://archive.ambermd.org/201112/0208.html
>>
>> I also read carefully this thread.
>> http://archive.ambermd.org/201205/0530.html
>>
>> Before starting simulations, I would be very grateful if people that
>> have been using these parameter sets would comment on their experience
>> with them (besides what is published in the respective references).
>>
>> If people are aware of other parameter sets, not available in the data
>> base but worth trying out, I would also be very interested.
>>
>> Best wishes
>> Vlad
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 28 2012 - 04:30:04 PDT
