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/>
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Received on Sat Jul 01 2017 - 18:00:05 PDT
