AMBER Archive (2006)

Subject: AMBER: RE: antechamber failure on FMN

From: Junmei Wang (
Date: Thu Aug 17 2006 - 18:14:47 CDT

Hi, David,
The current parameter set (APS.DAT)assumes a single bonded oxygen
attached to a carbon is more "favorable" than a carbon with total
valence of 3. This is why the bond assignment of FMNH.mol2 is not
correct. If one thinks the sybyl bond types in the input file are good,
or errors happen in bondtype running, one may try to run antechamber
with "-j 5" instead of "-j 4"(the default).

For some reasons, is not allowed to handle a system with an odd
number of electrons in the previous versions. In the latest version of
antechamber (Version 1.27, web release soon), we did some modification
so that (not divcon) can be applied to optimize systems with
odd number of electrons. A typical command is like the following:

$ACHOME/exe/antechamber -fi mol2 -fo mol2 -i FMNH.mol2 -o FMNH_bcc.mol2
-c bcc -j 5 -df 0 -nc -2 -m 2.

I also attached FMNH_bcc.mol2 with this email. I assumed the 2S+1 is 2
for FMNH.mol2, am I right?

All the best


Dear Junmei and Amber users,

I'm trying to use antechamber to parameterize the semiquinone form of
FMN (aka FAD); I've previously used it on the oxidized form. For those
not familiar with the molecule, it has three rings; in the oxidized
form, two of the rings have nitrogens double-bonded to carbons. The
semiquinone form gains an electron and a proton so one of these ring
nitrogens is now only single-bonded to carbons and also bonded to a

I'm attaching mol2 files of the oxidized (FMN.mol2) and semiquinone
(FMNH.mol2) forms to reproduce the problems I describe below. Both
should have a net charge of -2.

I'm having two basic problems, the second of which is more important:
(1) Bond typing fails for FMNH.mol2 -- that is, if I use antechamber to
judge the bond types and generate a new mol2 file (either from this mol2
file, or from a pdb file with all of the protons) I get out a mol2 file
that has incorrect bond types.
(2) Running antechamber on FMNH.mol2 gives an error about an odd number
of electrons, even though FMNH is different from FMN by gaining a proton
and an electron, even if I use the bond types in my mol2 file
(antechamber -i FMNH.mol2 -fi mol2 -o test.mol2 -fo mol2 -c bcc -j 1 -nc

Am I missing something obvious, or is there a problem with antechamber
here? I'm looking at a biochemistry book on metabolism and it shows FMN
and FMNH; I've got the bond types right on the rings.

Any suggestions will be greatly appreciated.


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