Re: [AMBER] antechamber no convergence

From: Jianhui Tian <>
Date: Mon, 16 Sep 2013 14:49:20 -0400

Dear David,

On Mon, Sep 16, 2013 at 10:13 AM, case <> 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.


> ...dac
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Sep 16 2013 - 12:00:03 PDT
Custom Search