AMBER Archive (2009)

Subject: [AMBER] bug in antechamber

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Jul 08 2009 - 11:19:12 CDT


Dear Junmei and all,

I believe I have found a bug in Antechamber/AmberTools (i.e. v. 1.27
of Antechamber, and also the more recent AmberTools release).

In particular, see the attached three mol2 files and try the following
sequence of commands:

antechamber -i 4-vinylpyridine_am1bcc_sybyl.mol2 -o out_sybyl.mol2 -fi
mol2 -fo mol2 -c bcc -at sybyl
antechamber -i 4-vinylpyridine_am1bcc_sybyl.mol2 -o out_sybyl_1.mol2 -
fi mol2 -fo mol2 -c bcc -at sybyl -j 1

(These two output files are attached, as is the input file).

In this case, the -j 1 option actually has no effect on atom/bond
typing as far as I can tell, as the output atom/bond types are the
same regardless of whether the j option is used.

HOWEVER (and here is the problem!) the -j 1 option has a huge effect
on the partial charge on the nitrogen atom.

Please advise.

Thanks,
David









David Mobley, Ph.D.
Assistant Professor of Chemistry
University of New Orleans
New Orleans, LA 70148
dlmobley_at_uno.edu
Office 504-280-6445
Fax 504-280-6860

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