Thanks, Daniel. I'll look at the RED website．
On , Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
> 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/).
> Hope this is helpful,
> -Dan
> 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.
> >
> > Yi An
> > Graduate Student
> > Department of Chemistry
> > Texas A&M University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Oct 31 2012 - 18:30:02 PDT
