Dear Francois,
Thanks a lot for your suggestions. I will try the building block approach.
J.
On Tue, Sep 17, 2013 at 3:11 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Jianhui Tian,
>
> Looking at this structure took 2 sec to be loaded in vmd, and by
> simply looking at this ATP analog:
>
> The problem you encounter was discussed several times & the answer is
> known:
>
> - problem of convergence? try a more robust program...
>
> - can you get an optimized structure? if yes, its conformation will be
> all, but representative...
>
> I would not optimize this type of whole molecule with multiple charge
> values. Instead I would use the building block approach; i.e. R.E.D.
> Server & R.E.D. IV and not antechamber in this type of work...
>
> See http://q4md-forcefieldtools.org/REDDB/projects/F-90/
>
> regards, Francois
>
>
> > Sorry to bother and take your time again.
> >
> > The no convergence happens during the sqm calculation for charge.
> > Is it doable/reasonable to get the topology like this:
> > 1. calculate the topology for the AMP PNP with -2 charge (this charge can
> > converge)
> > 2. get the charges using another way
> > 3. fix the charges in the final topology file
> > The assumption I have here is the bonded and vdw parameter will not be
> > affected by the net charge of the ligand.
> >
> > Otherwise, I do not know how to run the antechamber in a
> > broke-up/step-by-step way.
>
>
>
> > On Mon, Sep 16, 2013 at 10:13 AM, case <case.biomaps.rutgers.edu> wrote:
> >
> >> On Fri, Sep 13, 2013, Jianhui Tian wrote:
> >> >
> >> > Please find in the attachment the PDB of AMPPNP I used. Thanks a lot
> for
> >> > your time and your kind help.
> >>
> >> This is a problem that requires more time than I have had so far. It
> may
> >> be a
> >> problem with the initial geometry. What I've found so far is that
> >> Gaussian09
> >> also fails with this input, and that PM6 seems OK, and can optimize the
> >> geometry fine. I've not yet had time to investigate other options; you
> >> might
> >> try geometry optimization at the PM6 level, then try using that for AM1
> >> calculations.
> >>
> >> Of course, in general, using gas-phase calculations for a -4 anion is a
> >> stretch. You might consider adding a proton and looking at the -3
> state,
> >> since the pKa of ATP is around neutral pH.
> >>
> >> ...dac
>
>
>
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Received on Tue Sep 17 2013 - 07:00:03 PDT
