here i am sending the file which i generated kindly guide error belong to
these file
On Wed, Jul 5, 2017 at 2:16 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> 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
>>
>
>
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Received on Wed Jul 05 2017 - 11:30:03 PDT
