[gmx-users] GAFF

[日産化学 石川誠]

Dear David Mobley,

Thank you a lot.
I'll check antechamber.
Could you send me a script?

MAKOTO ISHIKAWA

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David Mobley
> Sent: Thursday, March 16, 2006 9:05 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] GAFF
> 
> 
> GAFF is the Generalized Amber Force Field, and contains AMBER 
> force field parameters for a lot of small molecules. The 
> AMBER force field itself has been ported to GROMACS by the 
> Pande group, but the last time I checked they had no plans to 
> port GAFF.
> 
> However, I do currently use GAFF with GROMACS by setting up 
> small molecules using the antechamber package (which is 
> distributed with AMBER, or can be downloaded directly from 
> the Antechamber web page). Then, we have a conversion script 
> we've written together with the Pande group which can turn 
> AMBER topology and coordinate files in to GROMACS topology 
> and coordinate files. So my approach is to run small 
> molecules through ANTECHAMBER to get GAFF parameters and then 
> convert their topologies to GROMACS.
> 
> We'll probably be making the conversion script available on 
> the web (at the AMBER port website) in the near future (at 
> which point I'd send an e-mail to this list) but in the 
> meantime you can get a copy by e-mailing me directly. It is a 
> "use-at-your-own-risk" script, in that we don't guarantee it 
> works properly. However, it works fine for us.
> 
> Incidentally, if you use antechamber, you need at least 
> version 1.2.4, if I remember correctly. Previous versions 
> (such as that distributed with AMBER 8) omit some improper torsions.
> 
> Hope this helps.
> David Mobley
> Dill group
> UCSF
> 
> On 3/14/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > 日産化学　石川誠 wrote:
> > > Hi all,
> > >
> > > I'm searching forecefield for a small molecule.
> > > Dose anyone know how to get GAFF for GROMACS?
> > >
> > more info please
> >
> > > Thank you for your time.
> > >
> > > MAKOTO ISHIKAWA
> > >
> > >
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> >
> > --
> > David. 
> > 
> ______________________________________________________________________
> > __
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > 
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