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/>
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Received on Mon Jul 03 2017 - 12:00:02 PDT
