Hi Junmei,
This seems to have fixed the problem. Thanks!
Gabriel
On Thu, Feb 18, 2010 at 1:48 PM, Junmei Wang <Junmei.Wang.utsouthwestern.edu
> wrote:
> Hi, Gabriel
> I am sorry for not providing a quick solution for your problem. I found the
> best solution is not to do coding, but to modify the atom type definition
> file. I simply added two more lines to ATOMTYPE_GFF.DEF. Please see the
> attached file. Please let me know if the definition file works for you.
>
> Best
>
> Junmei
>
>
>
>
>
> >>> Gabriel Rocklin <gabriel.rocklin.ucsf.edu> 02/15/10 5:22 PM >>>
> Hi Junmei,
>
> Just wondering how the Antechamber fix is going, and if you've learned
> anything now about the scope of the problem.
>
> Thanks,
> Gabriel
>
> On Wed, Feb 10, 2010 at 9:24 AM, Gabriel Rocklin
> <gabriel.rocklin.ucsf.edu>wrote:
>
> > 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 Thu Feb 18 2010 - 15:30:03 PST
