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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Received on Wed Nov 07 2012 - 18:30:03 PST
