AMBER Archive (2009)

Subject: Re: [AMBER] ATP/GTP parameters

From: E.M. (
Date: Tue Dec 08 2009 - 22:36:19 CST

Cheers from the Canadian prairies :)

Hello Francois,

some time ago you sent to me mol files for ATP and GTP (dXYP{1,2},
XYP{1,2} ), I was wondering if you also have equivalent library files
with charges for ATP and GTP, AND two hydrogens added at the gamma
phosphates (will use with ff03) . . . I would appreciate this a lot.


Eduardo Mendez
Oh!, here is my email as gmail does work sometimes...

FyD wrote:
> 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:
> regards, Francois
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