Dear David,
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.
>
I have used many different configurations to feed in the AM1 calculation,
and all of them have failed. The PDB structure I attached before is the
most "extended" one, as I read previous posts saying that no convergence
might be related to not well relaxed.
I will try the PM6 level geometry optimization to see whether it can
improve the result.
> 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.
>
The pronation state in my calculation is desired to be -4.
Thanks for your time and help.
J.
> ...dac
>
>
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Received on Mon Sep 16 2013 - 12:00:03 PDT
