AMBER Archive (2009)

Subject: Re: [AMBER] ATP and GTP parameters

From: E.M. (pckboy_at_gmail.com)
Date: Thu Sep 03 2009 - 21:08:02 CDT

Hello!
I think my email address bounces messages with attachments :(
could you send me the said parameters (ff03 version) to my alternative
address?

eduardo.mendez_at_usask.ca

I would appreciate this (and cite the paper with the database too, LOL)

Eduardo
FyD 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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