original_pdb ox_H_renum.pdb
group_name ox
cut_off 2.8
ion_ids 3058
software_version gms
ion_mol2files FE.mol2
naa_mol2files HEM.mol2 OXY.mol2
frcmod_files HEM.frcmod OXY.frcmod
MCPB.py -i ox.in -s 1
this error come i dont understand what to do know kindly guide
It contains the residue 187-HEM as normal.
It contains the residue 189-OXY as normal.
Totally there are 74 atoms in the small model.
Totally there are 314 electrons in the small model.
***Creating the standard model...
It contains the residue 187-HEM as normal.
It contains the residue 189-OXY as normal.
It contains the residue 189-OXY as normal.
Totally there are 76 atoms in the standard model.
***Creating the large model...
It contains the residue 187-HEM as normal.
It contains the residue 189-OXY as normal.
Totally there are 74 atoms in the large model.
Totally there are 314 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 Wed, Jul 5, 2017 at 12:57 PM, Andrew Schaub <aschaub.uci.edu> wrote:
> There are no charges, but those will be added at a later step using MCPB,
> after the QM calculations. It is weird about the atom types, but I would
> use the .mol2 file that Prof Case generated for you with the gaff atom
> types (n1 and o). Ensure that when you do the QM charges that NO is bound
> to your heme, and ensure you are using the right multiplicity and oxidation
> state (Fe2+) for the complex. Your iron should be coordinated to six
> nitrogen atoms total (one from imidazole, one from NO, and four from the
> heme). Nitric oxide by itself would be a doublet I believe, but in
> combination with heme, I'm not sure what the multiplicity of that species
> is (low spin vs high spin).
>
> Andrew
>
> On Wed, Jul 5, 2017 at 9:19 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Wed, Jul 05, 2017, Rana Rehan Khalid wrote:
> > > >
> > > > > I use this command to convert NITRIC OXIDE containing pdb file to
> > mol2
> > > > >
> > > > > antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y
> >
> > I can't reproduce your result. I've attached the mol2 file I get with
> the
> > above command.
> >
> > Be sure that the antechamber tests are passing with your installation. I
> > used
> > AmberTools17, but nothing has changed from AmberTools16 that should be
> > relevant here. Probably worth double-checking your run.
> >
> > Maybe someone else on the list has seen all of the atom types get
> replaced
> > with the residue name, and can chime in here.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > 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
Received on Wed Jul 05 2017 - 11:30:02 PDT
