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.
>
>
>
>
>
>
>
> > _______________________________________________
>
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>
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>
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>
>
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Nov 07 2012 - 19:00:03 PST
