[AMBER] antechamber limitation on molecule size

From: <anyiphysics.gmail.com>
Date: Mon, 29 Oct 2012 19:37:25 +0000

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
Chemistry Department
Texas A&M University
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Received on Mon Oct 29 2012 - 13:00:05 PDT
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