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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> >>>>>>>>
> >>>>>>>>
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Received on Tue Jul 05 2016 - 10:30:02 PDT
