Re: AMBER: antechamber

From: Scott Brozell <>
Date: Wed, 5 May 2004 14:30:17 -0700

On Wed, 5 May 2004, Amber admin wrote:

> In default, antechamber will run bondtype if the file format (such as gout)
> does not provide this information.

Note that a more exact wording is
.... does not provide this information or if antechamber does not use the
bond connectivity information provided.
In particular, antechamber does not use PDB CONNECT records.

Scott Brozell

> The warning message means that bondtype
> program may not assign the bond types (according to am1-bcc definition)
> correctly. In most of cases, this error is caused by incorrect bond
> connectivity. Therefore in case of error happens, it is recommended to run
> separately programs (espgen, respgen, atomtype, prepgen etc) and do some
> manual revisions. Please go to trouble-shooting of antechamber homepage for
> details.
> Best regards
> Dr. Junmei Wang
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Received on Wed May 05 2004 - 22:53:01 PDT
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