AMBER Archive (2009)

Subject: Re: [AMBER] ATP and GTP parameters

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Sep 03 2009 - 06:54:13 CDT

could they be put on the Amber contributed parameters page?

On Thu, Sep 3, 2009 at 5:36 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> 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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