Thanks for this. Some thoughts below.
On Sat, Aug 8, 2009 at 8:55 AM, <gilbert.bluemarble.net> wrote:
> Hi Dave and Dave,
>
> The problem is not in the AM1 charges or the bond correction parameters
> but in
> the assignment of the bond types for the nitro group. If you run
> antechamber and
> ask for the output in antechamber format you see that both NO bonds are
> assigned
> a bond type of 2, but there is no parameter for 23 02 31 (N double bond O),
> and
> so you set the correction term to zero and get back the original AM1
> charges. If
> you use a bond type of 9, a delocalized bond, for the nitro group, then the
> bond
> correction term is -.1500 (230931 in the Bayley table), and when you use
> this
> correction factor you get the OEChem results. Since antechamber uses a
> delocalized nitrogen atom type it probably should use a delocalized bond
> type.
> In this case I think antechamber is wrong and OEChem is correct.
>
Right, so this is really a problem with bond typing in Antechamber then.
>
> It would be most useful to have a suite of molecules with assigned atom
> and
> bond types that correspond to the test suite used by Bayley et al in
> parameterizing the AM1BCC method. I wrote an email to the list last month
> pointing out that Antechamber did not reproduce the structure given in the
> Bayley paper (which is the only case I know of) and I have not had any
> response
> to that email. Even the Bayley example raises questions about atom typing -
> the
> nitrogen adjacent to the double bond in the six membered ring is types as a
> normal nitrogen instead of a delocalized nitrogen - that need to be
> discussed if
> you expect to get the same result from all the programs implementing
> AM1BCC.
>
I agree this is important.
David Mobley
>
> Kevin E. Gilbert
> Serena Software
> Quoting case <case.biomaps.rutgers.edu>:
>
> > On Fri, Aug 07, 2009, David Mobley wrote:
> > >
> > > I am attaching just one example of profound disagreement. The 2-
> > > nitrothiophene.mol2 file contains Bayly AM1-BCC partial charges (sybyl
> > > atom naming); 2-nitrothiophene_ante_amber.mol2 contains antechamber
> > > AM1-BCC partial charges (amber atom naming), and 2-
> > > nitrothiophene_oechem_amber.mol2 contains OpenEye AM1-BCC partial
> > > charges.
> >
> > David:
> >
> > Thanks for sending the example. Let's look at the nitrogen charge you
> > mention:
> > >
> > > In this example, the Antechamber AM1-BCC charges differ from the
> > > others by more than 0.3 e on the nitrogen alone.
> >
> > There are two possible origins for this. First, the AM1 Mulliken charge
> > might be different. We get 0.613 for the nitrogen Mulliken charge. I
> don't
> > know what the other programs give, but that would be interesting to
> check.
> > (For completeness, our minimized AM1 energy is 31.74.)
> >
> > Second, and more likely, is that the BCC corrections are the source of
> > the difference. Here are the corrections that Junmei's am1bcc program
> > provides:
> >
> > bond at1 at2 pre-charge correction post-charge
> >
> > 0 C1 N1 -0.4880 0.6130 -0.0452 -0.5332 0.6582
> > 1 C1 C2 -0.5332 -0.0680 0.0000 -0.5332 -0.0680
> > 2 C1 S1 -0.5332 0.7320 0.2699 -0.2633 0.4621
> > 3 N1 O1 0.6582 -0.3680 0.0000 0.6582 -0.3680
> > 4 N1 O2 0.6582 -0.3480 0.0000 0.6582 -0.3480
> > 5 C2 C3 -0.0680 -0.1690 0.0000 -0.0680 -0.1690
> > 6 C2 H1 -0.0680 0.1850 0.0000 -0.0680 0.1850
> > 7 C4 S1 -0.4420 0.4621 0.2699 -0.1721 0.1922
> > 8 C3 C4 -0.1690 -0.1721 0.0000 -0.1690 -0.1721
> > 9 C3 H2 -0.1690 0.1680 0.0000 -0.1690 0.1680
> > 10 C4 H3 -0.1721 0.1850 0.0000 -0.1721 0.1850
> >
> > Note that there is only a small correction (from the C1-N1 bond). We
> don't
> > apply any corrections for the N1-O1 or the N1-O2 bond -- that seems a
> little
> > odd(??), and may indicate that there is a difference between our table of
> > BCC
> > corrections and those that Chris or openeye are using.
> >
> > Of course, at this point, I should (and will!) go check the above bond
> > corrections against the original papers. But I'm travelling right now,
> > without access to the needed papers. So maybe Junmei or someone on the
> list
> > can continue this check.
> >
> > [as an aside: you can get the bond correction output above by setting the
> > "debug" flag in am1bcc.c. I've attached a patch file against the current
> > release that creates the above format, which is more readable than what
> is
> > there now....]
> >
> > ....regards...dac
> >
> >
>
>
>
>
>
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Received on Wed Aug 19 2009 - 22:22:45 PDT
