RE: AMBER: Problem using antechamber

From: Junmei Wang <>
Date: Fri, 29 Sep 2006 13:17:37 -0500

Hi, Gustavo,
In bondtype, Cl must have a valence of 1, this is why it gave a warning
message. You may first generate a mol2 or ac file (with resp charges)
and manually modify atom types/bond types if needed, then use prepgen to
produce a prepin file if prefer to.
Good luck



 -----Original Message-----
From: [] On Behalf
Of Gustavo Seabra
Sent: Friday, September 29, 2006 11:19 AM
Subject: AMBER: Problem using antechamber

        I'm trying to use antechamber to generate parameters for ClO4-.
        I used the following procedure:
        1. from a pdb file, create a gaussina input using antechamber:
        $ antechamber -i PCL-.pdb -fi pdb -o -fo gcrt -nc -1
        2. Run the gaussian calculation
        3. Use antechamber to generate the prepin file. Here's where I
get the error:
        $ antechamber -i pcl-.log -fi gout -nc -1 -rn pcl- -o
pcl-.prepin -fo prepi -c resp
        Warning: the assigned bond types may be wrong, 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
        (4) increase PSCUTOFF in define.h and recompile bondtype.C
            Be cautious, use a large value of PSCUTOFF (>10) will
significantly increase the computer time
        Error: cannot run "/scr/arwen_2/seabra/amber10/exe/bondtype -i
judgebondtype() of antechamber.c properly, exit
        Am I doing something wrong here?
        P.S.: I know that the parameters for this ion are available in
the Amber parameter database. I'm trying to learn here...

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Received on Sun Oct 01 2006 - 06:07:19 PDT
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