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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Received on Thu Jun 30 2016 - 10:00:03 PDT
