David,
On 5/18/07, David van der Spoel <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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