AMBER: problems of antechamber

From: liu junjun <>
Date: Thu, 17 Jan 2008 21:15:54 -0500

Dear Amber:
    Thanks for your program of antechamber.
     I have encountered a question the day before yesterday when I
used the antechamber to prepare the prepi file of a small molecular
which is high-charged with -6 electrons. I assigned the am1-bcc
charges to the molecular and the error information is that:

Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C

    However the prepi file can be made by antechamber. But when I do
the molecular dynamic simmulation, the small molecular cannot be
minimized normally, two atoms bumped with each other. The item of 1-4
EEL = ************
    Now I give you the mol2 file of this molecular for your check.
With best regards.

Xi Chen

College of Chemistry, Huazhong Normal University
Wuhan, 430079, China

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Received on Sun Jan 20 2008 - 06:07:20 PST
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