dmobley at gmail.com
Mon May 21 17:52:55 CEST 2007
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.
> 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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