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
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> >>>>>>>> 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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> >>>>>>>
> >>>>>>
> >>>>> _______________________________________________
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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/>
> >>>> _______________________________________________
> >>>> AMBER mailing list
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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
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> >>> 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
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> >>
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Received on Mon Jul 03 2017 - 11:30:02 PDT
