AMBER Archive (2009)

Subject: Re: [AMBER] ATP and GTP parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 03 2009 - 04:36:45 CDT

Sergey,

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

I will send you these FF libraries to your email address.

regards, Francois

> 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

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