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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--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Fri Feb 19 2010 - 01:00:02 PST
