AMBER Archive (2009)

Subject: Re: [AMBER] ATP and GTP parameters

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Thu Sep 03 2009 - 01:35:33 CDT

Hi Francois,

I'd be also very grateful if you could send the link to all these
nucleotides libraries.

Thank you very much,

Sergey

E.M. wrote:
> Oh my!, do you have both?. This is even better =-O
> both states are great, although I will try first -2.
> I basically need to bind. ATP, ADP, GTP, GDP, AMP /GMP is not so
> useful now, but if you have them do share.
> which paper do I quote?.
>
> Regards
>
> Eduardo
> FyD wrote:
>> Eduardo,
>>
>>> I was wondering if anyone can supply parameters for the phosphates XYP
>>> with X={A,G}, Y={T,D,M} other than those
>>> found in http://www.pharmacy.manchester.ac.uk/bryce/amber
>>> I heard somebody has the parameters compatible with ff03, would you
>>> care to share those?
>>
>> ok no problem.
>>
>> Do you need dexoxyribose or ribose ?
>> Which protonation state for each terminal phosphate ? -2 or -1 ?
>>
>> regards, Francois
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber