Hi Fabricio,
Can you send these modeling files (including the Gaussian output files) to my email address? I can help to do a check.
Kind regards,
Pengfei
> On Jul 5, 2016, at 1:27 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
> There is one problem though. Lots of charges are 0. The copper charge is
> zero, the charges on the heavy atoms of the meth-Histidine are zero, the
> charges of some of the atoms on the other histidine are zero as are the
> ones on the tyrosine. My guess is that all atoms included in the small
> model for the gaussian calculation has had their charges set to zero.
> Maybe there is a problem with the RESP part?
>
> Fabrício
>
> 2016-07-05 14:16 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
>
>> Hello Pengfei. It worked. Now I can run MD with it.
>> Thank you very very much.
>>
>> On a second stage of my work, I'll need to add a superoxide radical (O=O.)
>> to the copper atom. I am not really sure how I'll do that. I'll come back
>> to our discussion when I get to that part. (which will be soon).
>>
>> Thanks again
>> Fabrício
>>
>> 2016-07-05 0:05 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>
>>> Hi Fabricio,
>>>
>>> Correction for the former email, it should be “there is no CT-NA related
>>> bond, angle and torsion parameters in the AMBER force field”.
>>>
>>> I have updated the new files and will send to you right now.
>>>
>>> Kind regards,
>>> Pengfei
>>>
>>>> On Jul 4, 2016, at 7:19 PM, Pengfei Li <ambermailpengfei.gmail.com>
>>> wrote:
>>>>
>>>> Hi Fabricio,
>>>>
>>>> You case is a little bit complicated. For your case is because you used
>>> the gaff atom type for the non-standard residues but it has connection with
>>> the normal amino acid which uses the AMBER atom types. People usually treat
>>> two unconnected parts with different atom type sets, for example, for a
>>> protein-ligand complex with the protein has AMBER atom type while ligand
>>> has gaff atom type.
>>>>
>>>> Marcelo’s method may be a way to solve the problem. You can also use
>>> antechamber to create mol2 for the non-standard residue using the AMBER
>>> atom type, and perform the MCPB.py commands again from the first step (this
>>> time you don’t need to re-run the Gaussian simulations because you have
>>> done that). However, this will still have problems since it is a little bit
>>> different from the AMBER atom type antechamber generated (for ff94, ff99,
>>> and ff99SB actually) and the ff14SB you are using (the former force fields
>>> don’t have CX atom type but ff14SB has). Meanwhile, there is no CT-NB
>>> related bond, angle and torsion parameters in the AMBER force field (since
>>> you had used a methyl group to replace a hydrogen in the HIS ring for your
>>> non-standard residue). I have created a new mol2 file and a new frcmod file
>>> for you based on my AMBER force field experience and will send to your
>>> email address, you can use them to begin the MCPB.py modeling process from
>>> the first step (again, this time you don’t need to re-run the Gaussian
>>> simulations because you have done that).
>>>>
>>>> Kind regards,
>>>> Pengfei
>>>>
>>>>> On Jul 4, 2016, at 4:02 PM, Marcelo Andrade Chagas <
>>> andrade.mchagas.gmail.com> wrote:
>>>>>
>>>>> Dear Fabrizio, good afternoon.
>>>>>
>>>>> I needed for a study I'm doing here to create a modified residue
>>>>> Lysine carboxylated attached to the enzyme active site.
>>>>>
>>>>> That is, in my case had a COO waste is not standard in the active site.
>>>>>
>>>>> When I see it looks similar to what you intend to do.
>>>>>
>>>>> First I did the following.
>>>>>
>>>>> I - I created a .pdb file with the waste that needed to modify (in my
>>> case
>>>>> the N atom appeared in the file attached to it three H atoms, as shown
>>>>> below;
>>>>> .
>>>>> .
>>>>> .
>>>>>
>>>>> .[image: Imagem intercalada 1]
>>>>>
>>>>>
>>>>>
>>>>> [image: Imagem intercalada 2]
>>>>>
>>>>>
>>>>> II - replaces this place for the group needed to put (COO), and used
>>>>> the following tutorial as a reference:
>>>>>
>>>>> http://ambermd.org/tutorials/advanced/tutorial1_adv/
>>>>>
>>>>> III - I had to parameterize Some constant values of strength and
>>> angle,
>>>>> and got
>>>>> charges for online server RED
>>>>>
>>>>> IV - I could create .frcmod and .mol2 files to this modified amino
>>> acid.
>>>>>
>>>>> You will need to do something, because when I use MCPB.py had to
>>> provide
>>>>> these input files (which for the modified amino acid residue
>>>>> They are understood in xleap as non-standard waste).
>>>>>
>>>>> See below my .in file for MCPB.py
>>>>> .
>>>>> .
>>>>> .
>>>>>
>>>>> [image: Imagem intercalada 3]
>>>>>
>>>>> Note that contains files related to what I am commenting.
>>>>>
>>>>>
>>>>> In my case, after using MCPB.py and get the files .mol2 the program
>>>>> LY1.mol2 created another file besides the other for other waste
>>>>> amino acids of the metal coordination sphere which I am using.
>>>>>
>>>>> You'll have to create a non-standard modified residue, as this modified
>>>>> residue should appear on the related site in your .pdb file protein
>>>>> all and has to be recognized with the parameters AMBER force field
>>>>> in xleap.
>>>>>
>>>>> I hope I have not acid very confusing to understand.
>>>>>
>>>>> Best regards
>>>>>
>>>>> Marcelo A. Chagas
>>>>>
>>>>> 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
>>>>>
>>>>> 2016-07-04 15:49 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
>>>>>
>>>>>> Hello again.
>>>>>> I was able to execute all steps of MCPB.py and generate the tleap.in
>>>>>> script, but there seems to be a problem with the modified Histidine
>>>>>> residue. There are no parameters for the bond between the carbonyl
>>> carbon
>>>>>> atom and the nitrogen of residue number 2 on the protein (there aren't
>>>>>> parameters for angles and dihedrals as well). Here is the tleap
>>> warning:
>>>>>>
>>>>>> Building bond parameters.
>>>>>> Could not find bond parameter for: c1 - N
>>>>>> Building angle parameters.
>>>>>> Could not find angle parameter: o - c1 - N
>>>>>> Could not find angle parameter: c1 - N - H
>>>>>> Could not find angle parameter: c1 - N - CX
>>>>>> Could not find angle parameter: c3 - c1 - N
>>>>>> Building proper torsion parameters.
>>>>>> ** No torsion terms for o-c1-N-H
>>>>>> ** No torsion terms for o-c1-N-CX
>>>>>> ** No torsion terms for c3-c1-N-H
>>>>>> ** No torsion terms for c3-c1-N-CX
>>>>>>
>>>>>> c1 (lower case c) refers to the histidine residue in question that was
>>>>>> originally considered a ligand and N (upper case N) is probably the
>>>>>> nitrogen atom of the residue to which this histidine is bonded to.
>>>>>> I'm not sure what CX refers to though.
>>>>>> There are some other problems also. The mol2 file for the Histidine
>>> has 0
>>>>>> charges for all heavy atoms.
>>>>>>
>>>>>> Any help here would be great.
>>>>>> Thank you
>>>>>> Fabrício
>>>>>>
>>>>>> 2016-07-01 20:29 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
>>>>>>
>>>>>>> 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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Received on Tue Jul 05 2016 - 18:30:02 PDT
