AMBER Archive (2006)

Subject: AMBER: antechamber and FMN

From: David Mobley (
Date: Tue Jun 06 2006 - 12:47:03 CDT

Dear Amber users,

I'm trying to use Antechamber (version 1.2.4) to parameterize FMN
(with am1-bcc charges), and I'm having some issues with atom typing of
one nitrogen. I am attaching a couple files to reproduce that
illustrate the problem.

Basically, if I begin with the same PDB file for FMN, and either:
(a) Run it directly into ANTECHAMBER, or
(b) Run it through OpenEye's convert
( to generate a mol2 file,
which I then put into ANTECHAMBER

I get two different atom types ("ne"="Inner sp2 N in conjugated
systems" versus "n2"="Aliphatic sp2 N with two connected atoms") for
the same nitrogen atom, although all of the other atom types are
identical. I wouldn't be terribly concerned, except the charges
assigned in the two cases are also quite different and opposite in
sign (ne with -0.4132; n2 with 0.0140), and obviously there are
corresponding differences in charges on adjoining atoms.

My understanding was that ANTECHAMBER should do the atom typing from
scratch, so it shouldn't in principle matter whether I use an input
mol2 file or an input pdb; I should end up with the same atom types.
Is this incorrect? If not, why am I getting two different atom types
beginning from the "same" structure, and which one is correct?

I'm attaching some relevant files:
1) test.pdb: The starting pdb file
2) test_am1bcc.mol2: The am1bcc mol2 file generated from test.pdb
using antechamber
3) test2.mol2: A starting mol2 file generated from test.pdb using
OpenEye's convert
4) test2_am1bcc.mol2: The am1bcc mol2 file generated from test2.mol2
using antechamber

Particularly notice atom 8 in #2 and #4; it is n2 in one, and ne in
the other, and, as I said, the charge is quite different.


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