[gmx-users] gromacs-antechamber-gaff

David Mobley dmobley at gmail.com
Mon May 21 19:15:59 CEST 2007


Francesco,

> At any event, one should be aware (if I understand
> correctly) that to convert from Amber to Gromacs with
> the alchemistry script below, one should have also the
> Amber code installed. Should it work at all with Amber
> 9, instead of the Amber 7 suggested.

Yes, this works with AMBER 7, 8, and 9 as far as I know (haven't used
with AMBER 7 myself, but have with 8 and 9). And yes, it does require
an AMBER installation. Someone is free to generalize it to not depend
on AMBER...

David


> In conclusion (if I understand) there might be a
> reason for such conversions if Gromacs code provides
> serious advantages (parallelization? I see a lot of
> warnings about this aspect, which with QM codes
> belongs to the far past) over Amber code.
>
> This is not endorsing any choice. I am still at the
> window (without "s").
>
> Cheers
> francesco pietra
>
>
>
> --- David Mobley <dmobley at gmail.com> wrote:
>
> > David,
> >
> > On 5/18/07, David van der Spoel
> > <spoel at xray.bmc.uu.se> wrote:
> > > Francesco Pietra wrote:
> > > > Planning to use gromacs aided by
> > antechamber/gaff for
> > > > my recurrent need of new bonded parameters, and
> > having
> > > > noticed that antechamber's tutorial refers to
> > Sybyl
> > > > and Gaussian, my question:
> > > >
> > > > Is it possible to use a QM suite different from
> > > > Gaussian? My own suite calculates perfectly RESP
> > and
> > > > CRESP. Or am I going to loose antechamber's
> > help? I am
> > > > prone to set manually, atom per atom, RESP or
> > CRESP
> > > > that I can calculate.
> > > >
> > > > Similarly, is it possible to use a non-Sybyl MM
> > > > package that also imports/saves pdb files?
> > > >
> > > > I know that one should come with precise
> > technical
> > > > questions, though, the above seem inescapable
> > > > problems/obstacles to me for accessing gromacs.
> > > >
> > > > Thanks
> > > >
> > > I haven't used it myself really, but some people
> > have (e.g. Fujitani et
> > > al, J. Chem. Phys. 123 084108 (2006)). You can use
> > antechamber to use
> > > your nonbonded atoms, but these have to be
> > compatible with the charges.
> > > So if you need to use another program than
> > Gaussian, you need to use the
> > >   recommended level of theory anyway. Since the
> > standard level of theory
> > > for GAFF is not extremely high, this should not be
> > a problem. Out of
> > > curiosity, which is your own suite?
> >
> > It occurs to me that you may want to add our
> > AMBER-to-GROMACS
> > converter tool to your contributions page (or at
> > least a link to where
> > it resides); I get lots of off-list e-mails asking
> > about it, and I
> > send it out a lot. It's at
> > http://www.alchemistry.org/FreeEnergyTools.
> >
> > Thanks,
> > David
> >
> > > --
> > > 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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