AMBER Archive (2009)

Subject: RE: [AMBER] ATP/GTP parameters

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Tue Sep 01 2009 - 11:29:59 CDT

Francois
The Duan et al. FF ff03, please.

Thanks, Steve

Steve Seibold
Research Asst. Professor
seibold_at_chemistry.msu.edu
19B Chemistry Building
Michigan State University
East Lansing, MI 48824
Office 517-355-9715 ext 264
 

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of FyD
Sent: Tuesday, September 01, 2009 12:26 PM
To: AMBER Mailing List
Subject: RE: [AMBER] ATP/GTP parameters

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_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]
> On Behalf Of FyD
> Sent: Monday, August 31, 2009 4:21 PM
> To: amber_at_ambermd.org
> Cc: q4md-fft_at_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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