[AMBER] bug in antechamber

From: David Mobley <dmobley.gmail.com>
Date: Wed, 8 Jul 2009 17:19:12 +0100

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.


Received on Wed Jul 08 2009 - 10:07:22 PDT
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