Hi Pengfei.
I have a question regarding the gaussian calculation of the large model.
From the input file, I can see that no geometry optimization is performed
on this model. I encountered convergence problems with this step. I am
guessing that, since the geometry of the complex obtained directly from the
pdb is not that great, the SCF routine has problems with convergence (hence
the XQC flag). Is that correct?
But even so, the large model gaussian calculation terminates with an error.
Is there something else I could do to fix this?
Thanks
Fabrício
2016-06-28 11:33 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Fabricio,
>
> I have modified MCPB.py code to make it can work for your case. And I have
> sent an email to your email address about that. Hope it helps.
>
> Kind regards,
> Pengfei
>
> > On Jun 27, 2016, at 3:56 PM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
> >
> > Hello. I've given up on using MCPB.py, and am trying to use MCPB instead.
> > I need to create a Histidine residue that has a methyl group bonded to
> the
> > epsilon nitrogen instead of the hydrogen that would be there.
> > So far I've tried to introduce a terminal CH3 with the command:
> >
> > addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.NE2 ag /NAME/CLR/HD1-1/.CD2
> tr
> > /NAME/CLR/HD1-1/.CE1 165.00
> >
> > This works fine, but the HE2 is still there. There is no command listed
> on
> > the manual to remove atoms. I could, change the HIE to a HID and transfer
> > the hydrogen to the other nitrogen atom, but the other nitrogen is bonded
> > to the metal ion.
> > Can I replace atoms or even remove them in MCPB?
> >
> > Thank you
> > Fabrício
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Received on Wed Jun 29 2016 - 10:00:02 PDT
