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, 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, 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
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Received on Fri Sep 11 2020 - 23:00:03 PDT
