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/>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jul 01 2017 - 18:00:03 PDT
