Re: [AMBER] antechamber limitation on molecule size

From: Daniel Roe <>
Date: Wed, 31 Oct 2012 18:06:57 -0600


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 R.E.D. server

Hope this is helpful,


On Wed, Oct 31, 2012 at 1:05 PM, Yi An <> 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 <150
> 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

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Oct 31 2012 - 17:30:03 PDT
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