Cheers Francois
I was wondering what kind of procedure you followed to compute the
charges of your parameter set of phosphates (the Duan et al. FF (ff03)),
with this I mean the optimization of the energy, was this a G9-N31 with
p and d?. I tried to repeat the parameter optimization but things did
not converge "there".
Regards
Eduardo
FyD wrote:
> Steve,
>
>> I would greatly appreciate that! Please do send the ATP, AMP, GTP,
>> GMP and finally dATP and dGTP libraries.
>
> Two force field topology databases are available: for (i) the Cornell
> et al. (ff94 up to ff99) or (ii) the Duan et al. FF (ff03).
>
> Which one do you want ?
>
> regards, Francois
>
>
>> -----Original Message-----
>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org]
>> On Behalf Of FyD
>> Sent: Monday, August 31, 2009 4:21 PM
>> To: amber.ambermd.org
>> Cc: q4md-fft.q4md-forcefieldtools.org
>> Subject: Re: [AMBER] ATP/GTP parameters
>>
>> Dear Steve,
>>
>>> I am looking for GTP parameters and looked in the achieves. I found
>>> that ATP and GTP had been deposited on the AMBER homepage site.
>>> However, looking through all the links, I cannot find them. Have
>>> they been incorporated into the newer force field/parameters? (I
>>> have AMBER 8 addition.)
>>
>> If you are interested I can send you ATP, GTP force field libraries or
>> any co-factors you might be interested in deriving from XYP (X = A, C,
>> T, G, dA, dC, dT, dG. Y = M D T Q etc... An even more...).
>>
>> This force field topology database has been developed in a single
>> R.E.D. job. Many co-factor analogs can be constructed since a building
>> block approach has been followed. See the list of cafactors built:
>> http://archive.ambermd.org/200812/0329.html
>>
>> regards, Francois
>
>
>
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Received on Wed Jan 13 2010 - 18:00:02 PST
