AMBER Archive (2006)

Subject: AMBER: antechamber failure on FMN

From: David Mobley (
Date: Tue Aug 15 2006 - 13:04:42 CDT

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 -2).

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.


  • application/octet-stream attachment: FMNH.mol2

  • application/octet-stream attachment: FMN.mol2
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