Dear David Mobley, Thank you a lot. I'll check antechamber. Could you send me a script?
MAKOTO ISHIKAWA > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] 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 <[EMAIL PROTECTED]> 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 > > > > > > > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please don't post (un)subscribe requests to the list. Use the www > > > interface or send it to [EMAIL PROTECTED] > Can't post? > > > Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > 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 > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > ++++++++++ > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [EMAIL PROTECTED] Can't post? > > Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
