AMBER Archive (2006)

Subject: AMBER: Re: antechamber failure on FMN

From: David Mobley (
Date: Fri Aug 18 2006 - 13:46:58 CDT


Thanks, I really appreciate it. The charges look great -- reasonable
based on FMN and FMNH2. I look forward to the release of the new
version of antechamber which can do these sort of calculations.


On 8/17/06, Junmei Wang <> wrote:
> 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
> Junmei
> 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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