Dear Fabrizio, good afternoon.
I'm also using MCPB.py program to study Bimetallic enzyme systems.
Today even managed to complete the steps until you reach the creation of
topology files and inicais speeds.
As for your question, the principle by which I understand is the following:
the most active site model you will make an optimization and then perform
a charge calculation. Because the key words (IOPS) used in the input if you
open
the output file .log corresponding gaussian in the / Initial Parameters
you will see that during the calculation of the sitema is frozen and
optimization is performed
only on the most external part of the system under study.
This is Pengfei?
Best regards
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-06-29 13:32 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
> 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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> >
> >
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Received on Wed Jun 29 2016 - 10:00:04 PDT
