I tried both systems fe----NO and Fe-----O2 same error come KeyError:
'O02' as mention above mail
one more thing i want to ask is that this fe is also make a bond with
histidine but when file prepare after cat command the bond between his and
fe not show only bond show is Fe---O2 show and Fe----NO show, no pyrol
ring heme bond with the fe show.
Protonation in fe---O2 system His 105 change to HID, while in FE----NO
system it change to HIE and Hydrogen add at the place which should make a
bond with FE. so i delete that hydrogen and convert the HIE to HID at 105
position. but i am confused that i Know that when NO bind with Fe then bond
break between Fe----HIS so in that case it may be right that MCPB.py show
after concatenation of all system. so may be above change i should not do.
kindly tell me
On Wed, Jul 5, 2017 at 2:21 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> 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 - 13:00:02 PDT
