[gmx-users] gromacs-antechamber-gaff

[Francesco Pietra]

Sorry to have been the spark for troubles. 

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.

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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