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
>> >>>>>>>>>>>> _______________________________________________
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Received on Wed Jul 06 2016 - 13:00:02 PDT
