Are you trying to run two different simulations? One with nitric oxide (NO)
bound? One with dioxygen (O-O) bound? If so, you can just change an oxygen
in your dioxygen bound complex to a nitrogen, save that and run MCPB ont
hat system as well. You would run both simulations, and then compare the
results of the two to look for differences. I believe the Poulos lab has
done some MD studies on NO in P450s:
https://www.ncbi.nlm.nih.gov/pubmed/26448477
https://www.ncbi.nlm.nih.gov/pubmed/27439869
Fortunately heme-bound enzymes are very well studied (for example myoglobin
and hemoglobin), so there is a wealth of information on electronic
structure calculations and molecular dynamics simulations. Those two review
papers I mentioned from ACS Chem Rev is a good place to start. I would
recommend searching the primary literature to see what protocols and
methods others have used to study heme bound systems to get an idea of what
type of analysis or system setups you will need to perform. I just wanted
to warn you, I've had limited experience with heme simulations, and have
found them to be very inflexible, and almost rock-like compared to other
enzymes I have studied in silico. I had to use accelerated sampling
techniques to get useful data.
Good Luck!
Drew
On Thu, Jun 29, 2017 at 10:03 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> Andrew one more thing i want to ask , i prepare the file for heme
> containing protein but in our case the heme fe-----NO in one system and
> other it bonded with O2 how i can add it because i need to study when NO
> attach AND when O2 attach what changes occur so in that case how i add NO
> and O2 in the system
>
> On Fri, Jun 30, 2017 at 12:38 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
> > That's great
> >
> > On Jun 30, 2017 12:30 AM, "Andrew Schaub" <aschaub.uci.edu> wrote:
> >
> >> As Elvis stated. You need Gaussian. But good news, The University of
> >> Michigan has access to it. http://arc-ts.umich.edu/software/gaussian/
> >>
> >> Best Regards,
> >>
> >> Drew
> >>
> >>
> >> On Thu, Jun 29, 2017 at 9:15 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> >> wrote:
> >>
> >> > this command is not working Andrew i am using amber 16 is go3 not
> >> buitin
> >> > i have all the input files for this command
> >> >
> >> > g03 < 4ZF6_small_opt.com
> >> > <http://ambermd.org/tutorials/advanced/tutorial20/files/
> >> > mcpbpy_heme/4ZF6_small_opt.com>
> >> > > 4ZF6_small_opt.log
> >> >
> >> > On Thu, Jun 29, 2017 at 11:30 PM, Rana Rehan Khalid <
> rrkhalid.umich.edu
> >> >
> >> > wrote:
> >> >
> >> > > oh yes it run now. Andrew i use
> >> > >
> >> > > 2.000000 charge for FE ferrous oxidation state
> >> > >
> >> > > and use 2.8 cutoff by default from the 4ZF6 <
> >> > http://ambermd.org/tutorials/advanced/tutorial20/files/mcpbp
> >> y_heme/4ZF6.in>.in
> >> > file. is it write ??
> >> > >
> >> > >
> >> > > On Thu, Jun 29, 2017 at 11:18 PM, Andrew Schaub <aschaub.uci.edu>
> >> wrote:
> >> > >
> >> > >> Based off of your output, and lack of an .input file, I am assuming
> >> the
> >> > >> following. You most likely copied the input script from the
> tutorial,
> >> > but
> >> > >> forgot to change the ions_id.
> >> > >>
> >> > >> original_pdb 4ZF6_H_renum.pdb
> >> > >> group_name 4ZF6
> >> > >> cut_off 2.8
> >> > >> *ion_ids 7440*
> >> > >> software_version g09
> >> > >> ion_mol2files FE.mol2
> >> > >> naa_mol2files HEM.mol2 1PE.mol2 EDO.mol2
> >> > >> frcmod_files HEM.frcmod 1PE.frcmod EDO.frcmod
> >> > >>
> >> > >> If you open up your HNOXO_H_renum.pdb, scroll down to where the Fe
> >> is,
> >> > and
> >> > >> find the atom number. Change your ions_id to match the atom number
> >> > there.
> >> > >> In the original tutorial, the Fe atom ID was pulled from
> >> > 4ZF6_H_renum.pdb,
> >> > >> by finding this line in the PDB file:
> >> > >>
> >> > >> HETATM *7440 FE* FE A 462 -7.890 0.888 28.105 1.00
> >> > >> 38.80 FE
> >> > >>
> >> > >> Best Regards,
> >> > >>
> >> > >> Drew
> >> > >>
> >> > >>
> >> > >>
> >> > >>
> >> > >> On Thu, Jun 29, 2017 at 7:44 PM, Rana Rehan Khalid <
> >> rrkhalid.umich.edu>
> >> > >> wrote:
> >> > >> >
> >> > >> > 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 : HNOXO_H_renum.pdb
> >> > >> > The variable add_bonded_pairs is : []
> >> > >> > The variable additional_resids is : []
> >> > >> > The variable anglefc_avg is : 0
> >> > >> > The variable bondfc_avg is : 0
> >> > >> > The variable cut_off is : 2.8
> >> > >> > The variable chgfix_resids is : []
> >> > >> > The variable force_field is : ff14SB
> >> > >> > The variable frcmodfs is : ['HEM.frcmod']
> >> > >> > The variable gaff is : 1
> >> > >> > The variable group_name is : HNOXO
> >> > >> > The variable ion_paraset is : CM (Only for nonbonded model)
> >> > >> > The variable large_opt is : 0
> >> > >> > The variable lgmodel_chg is : -99
> >> > >> > -99 means program will assign a charge
> automatically.
> >> > >> > The variable naa_mol2files is : ['HEM.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
> >> > >> > -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
> >> > >> > Traceback (most recent call last):
> >> > >> > File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 498, in
> >> > >> <module>
> >> > >> > addbpairs)
> >> > >> > File
> >> > >> >
> >> > >> "/home/rehan/Downloads/amber16/lib/python2.7/site-packages/
> >> > >> mcpb/gene_model_files.py",
> >> > >> > line 50, in get_ms_resnames
> >> > >> > resid = mol.atoms[i].resid
> >> > >> > KeyError: 7440
> >> > >> > _______________________________________________
> >> > >> > AMBER mailing list
> >> > >> > AMBER.ambermd.org
> >> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >>
> >> > >>
> >> > >>
> >> > >>
> >> > >> --
> >> > >> Andrew Schaub
> >> > >> Graduate Program in Chemical & Structural Biology
> >> > >> Tsai Lab, http:///www.tsailabuci.com/
> >> > >> Luo Lab, http://rayl0.bio.uci.edu/html/
> >> > >> University of California, Irvine
> >> > >> Irvine, CA 92697-2280
> >> > >> 949-824-8829 (lab)
> >> > >> 949-877-9380 (cell)
> >> > >> aschaub.uci.edu
> >> > >> _______________________________________________
> >> > >> 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
> >> >
> >>
> >>
> >>
> >> --
> >> Andrew Schaub
> >> Graduate Program in Chemical & Structural Biology
> >> Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
> >> Luo Lab, http://rayl0.bio.uci.edu/html/
> >> University of California, Irvine
> >> Irvine, CA 92697-2280
> >> 949-824-8829 (lab)
> >> 949-877-9380 (cell)
> >> aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/
> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> _______________________________________________
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>
--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Fri Jun 30 2017 - 00:00:02 PDT
