It is just an organic molecule with lots of fused aromatic rings. You can
see the pdb in attachment. Actually I don't know any methods to reduce it
into smaller building blocks. If you know how to do this please teach me.
Thanks a lot.
Yi
On Wed, Nov 7, 2012 at 8:34 PM, Aron Broom <broomsday.gmail.com> wrote:
> what is your 150 atom molecule? You're confident there is no reasonable
> method for reducing it to smaller building blocks?
>
> ~Aron
>
> On Wed, Nov 7, 2012 at 9:21 PM, <anyiphysics.gmail.com> wrote:
>
> > Hi Francois,
> >
> > Thanks a lot for your reply. But I still have a question: To derive
> charges
> > for central/terminal fragment of a molecule, I need a P2N file first.
> > However, since my molecule is bigger than 150 atoms, I cannot use
> ante-RED
> > to get the P2N file. If I don't have the P2N file, how can I break it
> into
> > fragments? If you know the answer please help me. Thank you.
> >
> > Yi
> >
> > On , FyD <fyd.q4md-forcefieldtools.org> wrote:
> > > Dear Daniel Roe and Yi An,
> >
> >
> >
> > > > I think 150 atoms is much larger than anything antechamber was
> >
> > > > designed to parameterize off the bat. Something like that you would
> >
> > > > typically break down into smaller chemical components and then
> >
> > > > parameterize those (analogous to breaking down a peptide into smaller
> >
> > > > amino acid chunks instead of trying to parameterize the whole thing).
> >
> > > > A good resource for stuff like this is something like RED server
> >
> > > > (http://q4md-forcefieldtools.org/REDS/).
> >
> >
> >
> > > I think one should always consider splitting a large molecule into
> >
> > > smaller elementary building blocks and generate the corresponding
> >
> > > molecular fragments when one wants to parameterize a large molecule.
> >
> > > RED and RED Server are specially designed for this task.
> >
> > > See http://q4md-forcefieldtools.org/REDDB/projects/F-90/ for instance.
> >
> >
> >
> > > RED Server at http://q4md-forcefieldtools.org/REDS/ is limited to
> >
> > > 150 atoms.
> >
> > > See http://q4md-forcefieldtools.org/REDS/faq.php#17; we can obviously
> >
> > > postpone this limit if this is needed by the user; just send a request
> >
> > > to contact_at_q4md-forcefieldtools.org.
> >
> >
> >
> > > RED Server Development at
> >
> > > http://q4md-forcefieldtools.org/REDS-Development/faq.php#17 is limited
> >
> > > to 350 atoms; This web server handle all the elements of the periodic
> >
> > > tables and is mostly designed for metal complexes. It can be obviously
> >
> > > used for organic molecules but ambiguities between atom names are not
> >
> > > well handled (CA is recognized as a Calcium atom and not as a C alpha
> >
> > > carbon). This is handled within the new RED version in preparation.
> >
> >
> >
> > > regards, Francois
> >
> >
> >
> >
> >
> > > > On Wed, Oct 31, 2012 at 1:05 PM, Yi An anyiphysics.gmail.com> wrote:
> >
> > > >> Hi all,
> >
> > > >>
> >
> > > >> I'm now using antechamber to derive partial charges for some large
> > > organic
> >
> > > >> molecules. My input file is pdb and I want to get mol2 files for
> these
> >
> > > >> molecules. My problem is when the molecule contains more than 150
> > > atoms, I
> >
> > > >> can only get the sqm.out file. I can't get the mol2 file even though
> > > the
> >
> > > >> sqm.out says the geometry is converged. However, if the molecule has
> > > >> atoms then I don't have this problem.
> >
> > > >>
> >
> > > >> The method I use in antechamber is AM1 and the commands
> > > are "antechamber -i
> >
> > > >> XXX.pdb -fi pdb -o XXX.mol2 -fo mol2 -c bcc -s 2". Does anyone know
> if
> >
> > > >> antechamber has a limitation on molecule size? Any related
> information
> > > is
> >
> > > >> appreciated. Thanks.
> >
> >
> >
> >
> >
> >
> >
> > > _______________________________________________
> >
> > > AMBER mailing list
> >
> > > AMBER.ambermd.org
> >
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Wed Nov 07 2012 - 19:30:02 PST
