Hi Vaibhav,
> On Sep 20, 2020, at 2:54 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> Dear Pengfei Li and Amber community,
> I have a query regarding the role and expected names for the gaussian log
> and fchk files required for MCPB.py steps 2 and 3.
> I'm assuming that the small_opt fchk and log files generated from the g09
> job are both important for step 3.
>
The small model opt fchk file will be used only in step 2 (I assumed you used the Seminario method, whereas if you use the Z-matrix method, the small model log file will be used in step 2), and the large model log file will be used only in step 3.
> I ran the small model g09 calculation, but the geometry changed
> significantly where carboxylate of HEM formed (unexpected) H-bond with H of
> HIS.
> Thus I ran another job after freezing the HIS-N*H* hydrogen, and
> carboxylate carbons (*C*OO) which finished correctly (this I named
> prot_small_opt2.log). Then generated the fchk file from the
> prot_small_opt2.chk file. As a result, I have two log files for small_opt
> jobs.
No matter what procedure you use, finally you need to make sure that you get a local minima for the small model, and the corresponding coordinates and Hessian information stored in the fchk file (I assumed you used the Seminario method) which you are going to use for the MCPB.py modeling.
> Large model g09 job is running at the time of writing this.
>
> The script doesn't require to explicitly specify the names of the log and
> fchk files to be read.
> Thus, will the script work as expected in the presence of multiple
> small_opt log files in the same folder?
Unless specified, the script will read the one with name as {group_name}_small_opt.fchk in the working folder.
But there is an option to specify the fchk/log file you want to use specifically (through the --fchk option for the fchk file, and through the --logf file option for the log file), as shown in the MCPB.py usage:
Usage: MCPB.py -i input_file -s/--step step_number
[--logf Gaussian/GAMESS-US output logfile]
[--fchk Gaussian fchk file]
Options:
-h, --help show this help message and exit
-i INPUTFILE Input file name
-s STEP, --step=STEP Step number
--logf=LOGFILE Gaussian/GAMESS-US output logfile
--fchk=FCHKFILE Gaussian fchk file
In this way, you do not have to rename the file, but just to tell MCPB.py about the file name directly.
Hope it helps,
Pengfei
>
> On Sat, Sep 12, 2020 at 4:59 PM Vaibhav Dixit <vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>>
> wrote:
>
>> I found HEM mentioned in the FE.mol2 file, which after correction to FE
>> does not give this error and I'm able to complete the tutorial as expected.
>> thank you.
>>
>> On Sat, Sep 12, 2020 at 7:51 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
>> wrote:
>>
>>> Dear Pengfei Li and Amber community,
>>> thanks for sharing this link and suggestions.
>>> I have begun trying this tutorial but I got error message on the terminal
>>> while running the first step in MCPB.py commands shown below.
>>> I'm using AMBER18.
>>> Can you please suggest what might be cause of this error and how can I
>>> fix it to get the expected result?
>>> thank you and best regards.
>>>
>>> (base) [exx.c107739 MCBP-CYP450]$ MCPB.py -i 4ZF6.in -s 1
>>> ******************************************************************
>>> * Welcome to use the MCPB.py program *
>>> * Version 5.0 *
>>> * Author: Pengfei Li *
>>> * Merz Research Group *
>>> * Michigan State University *
>>> * AND *
>>> * Hammes-Schiffer Research Group *
>>> * Yale University *
>>> ******************************************************************
>>> The input file you are using is : 4ZF6.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>> The following is the input variable you have:
>>> The variable ion_ids is : [7440]
>>> The variable ion_info is : []
>>> The variable ion_mol2files is : ['FE.mol2']
>>> The variable original_pdb is : 4ZF6_H_renum.pdb
>>> The variable add_bonded_pairs is : []
>>> The variable add_redcrd is : 0
>>> The variable additional_resids is : []
>>> The variable anglefc_avg is : 0
>>> The variable bondfc_avg is : 0
>>> The variable chgfix_resids is : []
>>> The variable cut_off is : 2.8
>>> The variable force_field is : ff14SB
>>> The variable frcmod_files is : ['HEM.frcmod', '1PE.frcmod', 'EDO.frcmod']
>>> The variable gaff is : 1
>>> The variable group_name is : 4ZF6
>>> The variable ion_paraset is : CM (Only for nonbonded model)
>>> The variable large_opt is : 0
>>> The variable lgmodel_chg is : -99
>>> The variable lgmodel_spin is : -99
>>> -99 means program will assign a charge automatically.
>>> The variable naa_mol2files is : ['HEM.mol2', '1PE.mol2', 'EDO.mol2']
>>> The variable scale_factor is : 1.0
>>> ATTENTION: This is the scale factor of frequency. The
>>> force constants will be scaled by multiplying the square
>>> of scale_factor.
>>> The variable smmodel_chg is : -99
>>> The variable smmodel_spin is : -99
>>> -99 means program will assign a charge automatically.
>>> The variable software_version is : g09
>>> The variable sqm_opt is : 0
>>> The variable water_model is : TIP3P
>>> The variable xstru is : 0
>>> ******************************************************************
>>> * *
>>> *=======================Metal Site Information===================*
>>> * *
>>> ******************************************************************
>>> ***Selected Metal ion FE is atom 7440 in residue 462-FE
>>> 400-CYM.SG is in 2.8 Angstrom of or set bonded (in the input file) to
>>> (one of) these metal ions
>>> 461-HEM.NA is in 2.8 Angstrom of or set bonded (in the input file) to
>>> (one of) these metal ions
>>> 461-HEM.NB is in 2.8 Angstrom of or set bonded (in the input file) to
>>> (one of) these metal ions
>>> 461-HEM.NC is in 2.8 Angstrom of or set bonded (in the input file) to
>>> (one of) these metal ions
>>> 461-HEM.ND is in 2.8 Angstrom of or set bonded (in the input file) to
>>> (one of) these metal ions
>>> ***The following residues are in the Metal Site:
>>> Residue 400-CYM
>>> Residue 461-HEM
>>> Residue 462-FE
>>> Traceback (most recent call last):
>>> File "/usr/local/amber18/bin/MCPB.py", line 644, in <module>
>>> addred, lgchg, lgspin)
>>> File
>>> "/usr/local/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
>>> line 1692, in gene_model_files
>>> totchg = totchg + chargedict[mol.residues[i].resname]
>>> KeyError: 'FE'
>>> (base) [exx.c107739 MCBP-CYP450]$
>>>
>>> On Fri, Sep 11, 2020 at 5:27 AM Pengfei Li <ambermailpengfei.gmail.com>
>>> wrote:
>>>
>>>> Hi Vaibhav,
>>>>
>>>> You can also try the MCPB.py program to parameterize your Heme-His
>>>> system:
>>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <
>>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>.
>>>>
>>>> Pengfei
>>>>
>>>>> On Aug 19, 2020, at 9:56 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
>>>> wrote:
>>>>>
>>>>> I'm also planning to generate similar parameters for Heme-His system.
>>>>> This would need, I guess, generating a new residue for His bound to
>>>> Heme
>>>>> (e.g. HIH)
>>>>> But I suspect that other users on the list might have already done
>>>> this.
>>>>> I hope they would respond and share their experience here.
>>>>>
>>>>> On Wed, Aug 19, 2020 at 6:51 PM Mohamed M. Aboelnga <
>>>>> mohamedm.aboelnga.mail.concordia.ca> wrote:
>>>>>
>>>>>> Thanks for sharing this paper.
>>>>>>
>>>>>> I had read it before but preferred to use the bonded model to
>>>>>> parameterize my heme and have full control on the settings specially
>>>> mine
>>>>>> has a His-Fe bond unlike P450.
>>>>>>
>>>>>> In fact, I have used the MCPB tutorial successfully to parameterize
>>>> the
>>>>>> resting state heme and used the generated parameters for numerous MD
>>>>>> simulations. Now, I only need to know how to use it properly for
>>>> compound I
>>>>>> instead!
>>>>>>
>>>>>> Sincerely,
>>>>>> Mohamed M. Aboelnga, PhD
>>>>>> Horizon Postdoctoral Fellow
>>>>>> Centre for Research in Molecular Modeling (CERMM)
>>>>>> Department of Chemistry and Biochemistry
>>>>>> Concordia University, Montreal, Quebec, CANADA
>>>>>>
>>>>>> ________________________________
>>>>>> From: Vaibhav Dixit <vaibhavadixit.gmail.com>
>>>>>> Sent: August 19, 2020 12:11 AM
>>>>>> To: AMBER Mailing List <amber.ambermd.org>
>>>>>> Subject: Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound
>>>> I
>>>>>> (heme enzyme, P450)
>>>>>>
>>>>>> You might find the methodology of Shahrokh et al. for importing/using
>>>> HEME
>>>>>> parameters in tleap useful.
>>>>>> https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21922
>>>>>>
>>>>>>
>>>>>> On Tue, Aug 18, 2020 at 9:40 PM Mohamed M. Aboelnga <
>>>>>> mohamedm.aboelnga.mail.concordia.ca> wrote:
>>>>>>
>>>>>>> Hello Pengfei,
>>>>>>>
>>>>>>> I tried to follow your suggestion to have the bound oxygen to the Fe
>>>> as
>>>>>> an
>>>>>>> independent residue but I am not able to parameterize it. Once I use
>>>>>>> antechamber it gives an error saying "ERROR in xmin(): Too few
>>>> atoms.".
>>>>>> Let
>>>>>>> me know if I understood your suggestion properly and if there is
>>>> anything
>>>>>>> else I should do!
>>>>>>>
>>>>>>> Many thanks for your endless support!
>>>>>>>
>>>>>>>
>>>>>>> Sincerely,
>>>>>>> Mohamed M. Aboelnga, PhD
>>>>>>> Horizon Postdoctoral Fellow
>>>>>>> Centre for Research in Molecular Modeling (CERMM)
>>>>>>> Department of Chemistry and Biochemistry
>>>>>>> Concordia University, Montreal, Quebec, CANADA
>>>>>>>
>>>>>>> ________________________________
>>>>>>> From: Pengfei Li <ambermailpengfei.gmail.com>
>>>>>>> Sent: July 20, 2020 11:53 AM
>>>>>>> To: AMBER Mailing List <amber.ambermd.org>
>>>>>>> Subject: Re: [AMBER] How to deal with oxygen atom on Fe=O of
>>>> Compound I
>>>>>>> (heme enzyme, P450)
>>>>>>>
>>>>>>> Hi Thirakorn,
>>>>>>>
>>>>>>>> On Jul 9, 2020, at 6:59 AM, Thirakorn Mokkawes <
>>>>>>> thirakorn.mokkawes.manchester.ac.uk> wrote:
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I am new to AMBER field. I am working on P450 enzymes and
>>>> attempting to
>>>>>>> study the mechanisms through Compound I.
>>>>>>>>
>>>>>>>> I have the problem with generating the mol2 and frcmod files for the
>>>>>>> oxygen atom bound to Fe on heme as Compound I (Fe=O). I did the
>>>>>> parameters
>>>>>>> files for heme and Fe, but for the oxygen should I treat it as
>>>> another
>>>>>>> ligand, water, or include it in heme mol2.
>>>>>>>>
>>>>>>>
>>>>>>> You should treat the oxygen as an independent residue from Fe.
>>>>>>>
>>>>>>>> I tried to follow these 2 links:
>>>>>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
>>>>>>>>
>>>>>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm
>>>>>>>>
>>>>>>>> Another question is how to create the parameter for Cys-Fe?
>>>>>>>>
>>>>>>>
>>>>>>> MCPB.py can handle this case, it will recognize the CYM/CYS residue
>>>>>>> automatically as long as your PDB file is consistent with AMBER
>>>> naming
>>>>>>> scheme for amino acids (but you need to make sure the cysteine
>>>> residue
>>>>>> has
>>>>>>> the correct protonation state).
>>>>>>>
>>>>>>>> Thank you in advance for any help you can offer.
>>>>>>>>
>>>>>>>
>>>>>>> Pengfei
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Dr. Vaibhav A. Dixit,
>>>>>>
>>>>>> Visiting Scientist at the Manchester Institute of Biotechnology
>>>> (MIB), The
>>>>>> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>>>>>> AND
>>>>>> Assistant Professor,
>>>>>> Department of Pharmacy,
>>>>>> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>>>>>> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>>>>>> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>>>>>> India.
>>>>>> Phone No. +91 1596 255652,
>>>>>> Email: vaibhav.dixit.pilani.bits-pilani.ac.in,
>>>> vaibhavadixit.gmail.com
>>>>>> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
>>>>>> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>>>>>>
>>>>>> ORCID ID: https://orcid.org/0000-0003-4015-2941
>>>>>>
>>>>>> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>>>>>>
>>>>>> P Please consider the environment before printing this e-mail
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> Regards,
>>>>>
>>>>> Dr. Vaibhav A. Dixit,
>>>>>
>>>>> Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
>>>> The
>>>>> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>>>>> AND
>>>>> Assistant Professor,
>>>>> Department of Pharmacy,
>>>>> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>>>>> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>>>>> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>>>>> India.
>>>>> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
>>>>> Email: vaibhav.dixit.pilani.bits-pilani.ac.in <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>, vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>
>>>>> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
>>>>> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>>>>>
>>>>> ORCID ID: https://orcid.org/0000-0003-4015-2941
>>>>>
>>>>> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>>>>>
>>>>> P Please consider the environment before printing this e-mail
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>
>>>
>>> --
>>>
>>> Regards,
>>>
>>> Dr. Vaibhav A. Dixit,
>>>
>>> Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
>>> The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>>> AND
>>> Assistant Professor,
>>> Department of Pharmacy,
>>> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>>> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>>> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>>> India.
>>> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
>>> Email: vaibhav.dixit.pilani.bits-pilani.ac.in <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>, vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>
>>> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
>>> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>>>
>>> ORCID ID: https://orcid.org/0000-0003-4015-2941
>>>
>>> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>>>
>>> P Please consider the environment before printing this e-mail
>>>
>>>
>>
>> --
>>
>> Regards,
>>
>> Dr. Vaibhav A. Dixit,
>>
>> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
>> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>> AND
>> Assistant Professor,
>> Department of Pharmacy,
>> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>> India.
>> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
>> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
>> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile <http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile>
>> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ <https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/>
>>
>> ORCID ID: https://orcid.org/0000-0003-4015-2941 <https://orcid.org/0000-0003-4015-2941>
>>
>> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra <http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra>
>>
>> P Please consider the environment before printing this e-mail
>>
>>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in <mailto:vaibhav.dixit.pilani.bits-pilani.ac.in>, vaibhavadixit.gmail.com <mailto:vaibhavadixit.gmail.com>
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile <http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile>
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ <https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/>
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941 <https://orcid.org/0000-0003-4015-2941>
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra <http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra>
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Thu Oct 22 2020 - 15:00:02 PDT
