Not sure what you meant by "the most active site model you will make an
optimization and then perform a charge calculation". The large model has no
optimization flags in it, and so, "optimization is performed only on the
most external part of the system under study" does not seem to be valid.
Charge calculation for the large model is performed with the system as it
is. The coordinates are exactly the same before and after the simulation.
I had the same problem a few years back using MCPB. The way I solved it
back then was performing a geometry optimization on the large complex as
well. But the question is: Is the optimization of the large model prior to
charge calculation a valid option? How will it affect charged derivation
from the RESP procedure later on?
Fabrício
2016-06-29 13:57 GMT-03:00 Marcelo Andrade Chagas <andrade.mchagas.gmail.com
>:
> 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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Received on Wed Jun 29 2016 - 12:30:03 PDT
