AMBER: RE: antechamber and FMN

From: Junmei Wang <>
Date: Wed, 7 Jun 2006 15:39:48 -0500

Hi, David,
I guess you use "-j 5" flag for the mol2 file converted by OpenEye
(test2.mol2). Evidently, there are some problem with the atom types/bond
types for N1 and N4. And the middle ring should not be an aromatic ring.
If you are not sure if the mol2 file is good, try to use "-j 4" flag to
run the antechamber program.

All the best


Sent: Tuesday, June 06, 2006 12:47 PM
Cc: Junmei Wang; John Chodera
Subject: antechamber and FMN

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

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
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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jun 11 2006 - 06:07:09 PDT
Custom Search