[AMBER] antechamber limitation on molecule size

From: Yi An <anyiphysics.gmail.com>
Date: Wed, 31 Oct 2012 14:05:59 -0500

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
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Received on Wed Oct 31 2012 - 12:30:03 PDT
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