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 Mon Sep 16 2013 - 07:30:04 PDT
