I just wanted to add this to the list so it is archived..
---------- Forwarded message ----------
From: Gabriel Rocklin <gabriel.rocklin.ucsf.edu>
Date: Wed, Feb 10, 2010 at 9:24 AM
Subject: Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic?
To: Junmei Wang <Junmei.Wang.utsouthwestern.edu>
Thanks Junmei. The parameters do more than maintain the planar conformation
of the ring - they keep the ring substituents in plane with the rest of the
ring. I'm not actually interested in imidazole and imidazolium themselves,
but in their substituted versions, and binding free energies appear to
change significantly when the ring substituents are allowed to bend when in
protein complexes.
Hope to hear from you by Monday.
Gabriel
On Wed, Feb 10, 2010 at 8:07 AM, Junmei Wang <Junmei.Wang.utsouthwestern.edu
> wrote:
> Dear Gabriel,
> I will fix this no later than next Monday. Did you observe bizarre behavior
> of gaff for imidazolium? It is true that the torsional angle parameter of
> X-c2-na-X (2.5) is weaker than X-cc-na-X (6.8), but those parameters are
> simply used to maintain the planar conformation of the ring. The
> minimization or MD results of the two set of parameters should be very
> similar anyway.
>
> Best
>
> Junmei
>
> >>> Gabriel Rocklin <gabriel.rocklin.ucsf.edu> 02/10/10 12:56 AM >>>
> Dear Junmei,
>
> Do you have an estimate on how long that will take? I'd like to know
> whether I should try to develop a workaround, or whether I can wait for
> you.
> Also, it would be good to know what the scope of the problem is as soon as
> you've identified it, even if you haven't yet designed a fix.
>
> Thanks,
> Gabriel
>
>
>
> On Tue, Feb 9, 2010 at 9:07 PM, Junmei Wang
> <Junmei.Wang.utsouthwestern.edu>wrote:
>
> > Dear Gabriel
> > I got the same result as yours. It is not a correct antechamber behavior.
> I
> > will fix this bug as soon as possible. Thank you very much for reporting
> > this problem
> >
> > I really appreciate your great help
> >
> > Junmei
> >
> >
> > >>> Gabriel Rocklin <gabriel.rocklin.ucsf.edu> 02/09/10 1:33 AM >>>
> > Dear Junmei and others,
> >
> > I am getting strange results when trying to parameterize some
> heterocyclic
> > cations using antechamber. Using a mol2 file for imidazole, when I do-
> >
> > antechamber -i imidazole.mol2 -o imidazole_out.prepi -fi mol2 -fo prepi
> >
> > I get a prep file for imidazole that has ring atom types cc, cd, and na.
> > But when I do the same thing for imidazolium, I get atom types c2 and
> na.
> > Because GAFF c2 is not aromatic, the dihedral parameters about the ring
> > become significantly weaker. The protonation should not affect the
> > aromaticity like this, correct? I see the same thing
> > for constitutively charged, n-substituted imidazoliums, as well as for
> > thiazoles vs thiazoliums.
> >
> > Is this the correct antechamber / GAFF behavior? If so, why?
> >
> > I've attached the input and output files.
> >
> > Thanks,
> > Gabriel
> >
> > Gabriel Rocklin
> > UCSF Shoichet/Dill Labs
> >
> >
>
>
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Received on Wed Feb 10 2010 - 11:30:04 PST
