AMBER Archive (2006)

Subject: Re: AMBER: antechamber failure on FMN

From: David Mobley (
Date: Tue Aug 15 2006 - 13:16:47 CDT


OK, I have a little more on that. FMNH is supposed to be a neutral
radical, so one of the carbons has only three bonds. This is probably
the origin of the problem, which leads me to two further questions:

(1) Is there any way to deal with this in antechamber and any gaff
atom type for it? If not,
(2) If I do a Hartree-Fock 6-31G* calculation to calculate charges for
FMNH in its radical form, will antechamber be able to handle RESP


On 8/15/06, David Mobley <> wrote:
> 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
> proton.
> 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.
> Thanks,
> David
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