Hi Fabricio,
Please send me these files, I can help to do a check.
Kind regards,
Pengfei
> On Jul 6, 2016, at 3:51 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
> Hey Pengfei. Maybe you can help me with this. I have started parameterizing
> the system with an superoxide radical. Got up to the generation of the
> gaussian files without problems (renamed the Histidine residue NHIC, etc).
> The problem is not really amber related, it is more chemistry related I
> guess.
> The superoxide anion has a negative charge. So, in order to set the system
> charge for the gaussian models, I used the same charge I had for the
> previous system and just subtracted 1 (which results in charge 0).
> For this
> system, it also means that multiplicity has to be 2. The same reasoning
> should work for the large model, right? Since the small and large model
> have the same charge. Except, it does not seem so. Gaussian has complained
> that the large_mk.com with charge 0 and multiplicity 2 is incompatible. Any
> ideas on what is happening?
> If you prefer I can send you the files.
> Thank you
> Fabrício
>
> 2016-07-06 14:51 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
>
>> Hi Pengfei. I found what the problem was. When doing the large_mk
>> calculation, I had switched the IOP on the gaussian file from 6/33=2 to
>> 6/50=1. That aparently makes the log output file different. My guess is
>> that 6/50=1 redirects ESP information to a .gesp file and 6/33=2 keeps all
>> info in the gaussian log file.
>> I've redone the calculations and happily all the parameters were there.
>> The charges seem reasonable enough, but this alone, of course, is a matter
>> for debate.
>> Thank you again for all your help
>> Fabrício
>>
>> 2016-07-05 22:17 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>
>>> 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
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> AMBER mailing list
>>>>>>>>>>>>>>> AMBER.ambermd.org
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>>
>>>>>>>>
>>>>>>
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Received on Thu Jul 07 2016 - 14:00:03 PDT
