Hi Pengfei, just sent you the files.
Thank you very much.
Fabrício
2016-07-07 17:46 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
> 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
> >>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>>>
> >>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> _______________________________________________
> >>>>>>>>>>> AMBER mailing list
> >>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> AMBER mailing list
> >>>>>>>>> AMBER.ambermd.org
> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>
> <image.png><image.png><image.png>_______________________________________________
> >>>>>>>> AMBER mailing list
> >>>>>>>> AMBER.ambermd.org
> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>
> >>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 07 2016 - 14:00:04 PDT
