Hi Pengfei and Marcelo. Now I get it. Plus, I wrote to the gaussian guys to
ask why the large_mk.com calculation was terminating with an error "Error
termination via Lnk1e in /home/fabricio/g09/l602.exe at Mon". The answer
was to add a line with the name of the file into which the ESP charges will
be written. It is important to add a blank line between the Copper MKradius
value and to add two blank lines after the filename (I´ve tested a bit to
see if that really mattered).
Things seem to be getting on the right track now.
Thanks
Fabrício
2016-06-30 13:51 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Fabricio,
>
> I guess Marcelo's suggestion is about performing the partial optimization
> with only the external part being optimized but the central part being
> frozen.
>
> In Gaussian a frozen symbol -1 or optimize symbol 0 follows the element
> symbol and aheads the atomic coordinates is used to freeze/free certain
> atom(s) during the optimization. For example:
>
> C -1 0.000 0.000 0.000
> H 0 1.000 0.000 0.000
>
> means only optimize the position of H but freeze the position of C during
> the optimization (also don’t forget to use opt keyword in the Gaussian
> input file).
>
> Is that right? Marcelo.
>
> Kind regards,
> Pengfei
>
> > On Jun 29, 2016, at 12:57 PM, Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com> wrote:
> >
> > 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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> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
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Received on Fri Jul 01 2016 - 17:00:02 PDT
