Here's the file Junmei sent me. You'd have to ask him how it's going to be
distributed.
Gabriel
On Fri, Feb 19, 2010 at 3:48 PM, Gabriel Rocklin <grocklin.gmail.com> wrote:
> Hi there,
>
> I may have skipped part of this conversation, but where is the attached
> file? or at least the added lines. And if this fix will be available as a
> patch in AT 1.3 soon or later.
>
> Thanks,
>
> Alan
>
> On Thu, Feb 18, 2010 at 23:21, Gabriel Rocklin <gabriel.rocklin.ucsf.edu
> >wrote:
>
> *> 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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> *> AMBER.ambermd.org *
> *> http://lists.ambermd.org/mailman/listinfo/amber *
> *> *
>
> --
>
>
>
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Received on Fri Feb 19 2010 - 16:00:02 PST
