I'm confused. Are you trying to do the MCPB approach, or are you trying to
use the heme frcmod/prep file from the paper? Are you attempting to mix
these two approaches?
I would suggest before trying to run your own system, to run through a
couple of the basic tutorials, as well as the MCPB tutorial. Running
through the tutorials give you an overview of how all of these files are
setup, and how the entire system works. Attempting to run a complex
simulation like heme is not easy, but the tutorails will definitely help.
Please at least do the MCPB tutorial with the model system provided before
trying to load it with a dioxygen or nitric oxide species. You'll save
yourself a lot of time and headaches in the end.
Good Luck!
Drew
On Mon, Jul 3, 2017 at 11:51 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> i already apply for that. i read the tutorial as you guide me i want to
> know that
> A new atom type definition, if required, must be clear and precise. It
> should also be possible to treat the definition
> in an automatic atom-type assignment procedure. how i can make my pdb file
> compatible with frcmod and .in file
> I have the force field file frcmod for Heme ---O2 and prep file of it. and
> i tried manually change my pdb file to make it readable for frcmod and prep
> file but not succeeded actually i find form many places but i dont know how
> i use that particular frcmod file and prep file i load these file i follow
> source leaprc.protein.ff14SB
> source leaprc.gaff
> loadamberparams heme.frcmod
> loadamberprep heme.in
> loadpdb oxyheme.pdb
> tleap aborted with the error like hybridization sp2,sp3 type lines it maybe
> due to, that my pdb do not match with heme-fe---O2 force field which some
> one send me.
>
> Thanks
>
> On Mon, Jul 3, 2017 at 2:31 PM, Andrew Schaub <aschaub.uci.edu> wrote:
>
> > Rana,
> >
> > You are at the University of Michigan. You guys have Gaussian on the
> > cluster (ARC-TS). You can email them and they will get you set up with an
> > account and probably show you the basics of running a gaussian job. I
> > assume you are using the same cluster to run your AMBER jobs.
> >
> > Best Regards,
> >
> > Andrew
> >
> > On Mon, Jul 3, 2017 at 11:23 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > wrote:
> >
> > > is there any free tool for QM that uses the MCPB.py output file like
> Go3
> > > etc
> > >
> > > On Mon, Jul 3, 2017 at 1:05 PM, Pengfei Li <ambermailpengfei.gmail.com
> >
> > > wrote:
> > >
> > > > Hi Rana,
> > > >
> > > > I think you met similar problem as a former email which you sent to
> me
> > > > independently. The solution is similar. Please let me know your
> trying
> > > and
> > > > difficulties you met to solve the problem.
> > > >
> > > > Kind regards,
> > > > Pengfei
> > > >
> > > > > On Jul 1, 2017, at 8:40 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > > > wrote:
> > > > >
> > > > > after running this command i found this error """MCPB.py -i
> NO.in
> > > -s
> > > > > 1"""
> > > > > Totally there are 313 electrons in the large model.
> > > > > Traceback (most recent call last):
> > > > > File "/home/rehan/Downloads/amber16/bin/MCPB.py", line 562, in
> > > <module>
> > > > > premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg,
> lgchg)
> > > > > File
> > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site-
> > > > packages/mcpb/gene_model_files.py",
> > > > > line 1745, in gene_model_files
> > > > > ionids, chargedict, lgchg, outf, watermodel, largeopt, sqmopt)
> > > > > File
> > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site-
> > > > packages/mcpb/gene_model_files.py",
> > > > > line 1441, in build_large_model
> > > > > chargedict, IonLJParaDict, largeopt)
> > > > > File
> > > > > "/home/rehan/Downloads/amber16/lib/python2.7/site-
> > > > packages/msmtmol/gauio.py",
> > > > > line 156, in write_gau_mkf
> > > > > chg = int(round(chargedict[ionname], 0))
> > > > > KeyError: 'O02'
> > > > >
> > > > > On Sat, Jul 1, 2017 at 8:57 PM, Andrew Schaub <aschaub.uci.edu>
> > wrote:
> > > > >
> > > > >> You need to add the '-m' flag to specify your multiplicity.
> > Remember,
> > > > >> nitric oxide has one free electron as it's a radical, so it's at
> > > least a
> > > > >> doublet (and not a singlet). So adding '-m 2' would probably fix
> > your
> > > > >> problem. If you are just going to transfer the mol2 to the MCPB.py
> > > > script
> > > > >> then it's not neccessary to add charges.
> > > > >>
> > > > >> antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y
> > > > >>
> > > > >> On Sat, Jul 1, 2017 at 5:47 PM, Rana Rehan Khalid <
> > rrkhalid.umich.edu
> > > >
> > > > >> wrote:
> > > > >>
> > > > >>> I tried to produce the mol2 file for Nitric oxide (NO) following
> > > error
> > > > >> come
> > > > >>> kindly guide me
> > > > >>> antechamber -fi pdb -fo mol2 -i NIT_H_renum.pdb -o NIT.mol2 -c
> bcc
> > > -pf
> > > > y
> > > > >>> -nc 0
> > > > >>>
> > > > >>> Info: Bond types are assigned for valence state 2 with penalty
> of 3
> > > > >>> Total number of electrons: 15; net charge: 0
> > > > >>> INFO: Number of electrons is odd: 15
> > > > >>> Please check the total charge (-nc flag) and spin
> multiplicity
> > > (-m
> > > > >>> flag)
> > > > >>>
> > > > >>> Running: /home/rehan/Downloads/amber16/bin/sqm -O -i sqm.in -o
> > > sqm.out
> > > > >>> Error: cannot run "/home/rehan/Downloads/amber16/bin/sqm -O -i
> > > sqm.in
> > > > -o
> > > > >>> sqm.out" of bcc() in charge.c properly, exit
> > > > >>>
> > > > >>> On Fri, Jun 30, 2017 at 2:35 AM, Andrew Schaub <aschaub.uci.edu>
> > > > wrote:
> > > > >>>
> > > > >>>> 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
> > > > >>>>>>>
> > > > >>>>>>
> > > > >>>>> _______________________________________________
> > > > >>>>> 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
> > > > >>>>
> > > > >>> _______________________________________________
> > > > >>> 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
> > > > >>
> > > > > _______________________________________________
> > > > > 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
> > >
> >
> >
> >
> > --
> > 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
> >
> _______________________________________________
> 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/>
_______________________________________________
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Received on Mon Jul 03 2017 - 12:30:03 PDT
