Hi Fabricio,
> On Jun 29, 2016, at 3:00 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
> 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?
>
Yeah. It is a valid option. But care should be taken for checking whether the large model structure after optimization changed a lot. If there is a large conformation change, partial optimization is suggested (only optimize the hydrogen position, there is a variable in MCPB.py called large_opt, see page 289 of the manual: http://ambermd.org/doc12/Amber16.pdf <http://ambermd.org/doc12/Amber16.pdf>, can be used for this purpose).
Kind regards,
Pengfei
> 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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>>>>
>>>>
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Received on Thu Jun 30 2016 - 10:00:03 PDT
