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
> >>>>>>>>>>>> _______________________________________________
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> >>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>
> >>>>>>>>>>>
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> >>>>>>>>
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> >>>>>>>
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Received on Wed Jul 06 2016 - 11:00:03 PDT
