Hi Francois,
I will write a tutorial as soon as I finish this project (hopefully I can
finish this project). Thanks for your help.
Yi
On , FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Yi,
> > 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.
> Your molecule is just... great ;-) Nice project...
> We worked on highly similar projects about calixarenes
> http://en.wikipedia.org/wiki/Calixarene with or without metal ions.
> As usual, see projects in REDD.B. & in particular the 3 following
> projects:
> http://q4md-forcefieldtools.org/REDDB/projects/F-87/
> http://q4md-forcefieldtools.org/REDDB/projects/F-88/
> http://q4md-forcefieldtools.org/REDDB/projects/F-89/
> I definitively think you 'should' split this molecule into different
> building blocks; this is straightforward using RED Server/RED IV.
> You could even compare the two approaches (i) using the whole molecule
> (I can push back the 150 atoms limit of RED Server or you can use
> RED Server Dev.) and (ii) using the building blocks.
> About (i), the key is chemical equivalencing (Ante_R.ED 1.x from the
> RED tools III.x does NOT handle this case, and our algo. in RED
> Server/Ante_R.ED 2.0 is not well adapted to this case. I would be
> just curious to see what would be the answer from Antechember here...
> We can run the new algo. available in our new RED version and adapt
> the output to create a P2N file for RED IV if you need it.
> About (ii), your just create the elementary building blocks as
> originally defined in Cieplak et al.
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract (see
> also examples in REDD.B.). Once the RED Server job is done you
> reconstruct your pseudo-macromolecule using a LEaP script; see for
> instance:
> http://q4md-forcefieldtools.org/REDDB/projects/F-87/script1.ff
> The new RED version will reconstruct each macromolecule by itself;
> ie without LEaP.
> Your big molecule could be split into 4 elementary building blocks;
> may be more if you want to create analogs of this big molecule...
> (you could also consider adding extra-points & united carbons)
> You could write a nice tutorial here, and compare the whole molecule
> approach and its limitations versus the building block approach and
> its numerous advantages.
> regards, Francois
> > 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.
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Received on Thu Nov 08 2012 - 09:00:03 PST
