RE: AMBER: Antechamber

From: Junmei Wang <>
Date: Thu, 19 Apr 2007 08:58:14 -0500

Hi, John,
There is no limitation on molecular weight, even number of atoms in a
molecule. Please generate an ac or mol2 file with antechamber to double
check the connectivity. If you attach the file of the molecule, I can
help you to find the problem.
All the best

        Is there a molecular weight limitation in antechamber? I have
been trying to load a series of penicillins into antechamber. The
molecules with small side chains work just fine, but as the side chains
increase in size I get an antechamber message that says:


        For atom [11]:O the best APS is not aero, exit


        1) Double check the structure (the connectivity) and/or

        2) Adjust atom valence penalty parameters in APS.DAT,

        3) Increase MAXVASTATE in define.h and recompile

        4) Increase PSCUTOFF in define.h and recompile bondtype.C


        I have verified that the structures and connectivities are


        This seems to occur when the number of electrons in the system
exceeds 200.

        Can someone suggest a workaround for this?


        John Beale




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Received on Sun Apr 22 2007 - 06:07:29 PDT
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