Thanks Marcelo for the help.
Hi Fabricio,
The error seems relate to the atom recognition.
Can you send me an independent email with your original PDB, mol2 and MCPB.py input file? I can help to do a check.
Kind regards,
Pengfei
> On Jun 23, 2016, at 1:38 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
> Mistype...
>
> "MCPB.py -i Myprotein.pdb -s 1a" = "MCPB.py -i Myprotein.in -s 1a"
>
> 2016-06-23 14:27 GMT-03:00 Marcelo Andrade Chagas <andrade.mchagas.gmail.com
>> :
>
>> Dear, good afternoon.
>>
>> At first his command is wrong from what I understand.
>>
>> check this first.
>>
>> Your .in file (not what you put into what looks like a pdb file)
>> It must contain a type structure:
>>
>> MCPB.py -i 1OKL.in -s 1a
>>
>>
>> [image: Imagem intercalada 1]
>>
>> See this appears demonstrated in the tutorial, as follows.
>> Did you see this?
>>
>> [image: Imagem intercalada 2]
>>
>> Regards,
>>
>> Marcelo A. Chagas
>>
>> Marcelo Andrade Chagas, MSc
>> (PhD student)
>> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
>> * http://lqcmm.qui.ufmg.br/
>> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
>> Tel:(31)3409-5776
>>
>> 2016-06-23 13:19 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
>>
>>> Hello. I am trying to follow the MCPB.py tutorial for parameterizing the
>>> metal center on an enzyme. The metal center is comprised of a Copper atom
>>> bonded to 2 histidines. One of these His, is linked to the metal in a
>>> non-standard way, so I have treated is like the LIGAND in the tutorial.
>>> I have followed the tutorial exactly as it is, only, when I get to the
>>> MCPB.py command "MCPB.py -i Myprotein.pdb -s 1a", I get the following
>>> error.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *Traceback (most recent call last): File
>>> "/home/fabricio/amber16/bin/MCPB.py", line 562, in <module> premol2fs,
>>> cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg) File
>>>
>>>
>> "/home/fabricio/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/fabricio/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
>>> line 1441, in build_large_model chargedict, IonLJParaDict, largeopt)
>>> File
>> "/home/fabricio/amber16/lib/python2.7/site-packages/msmtmol/gauio.py",
>>> line 156, in write_gau_mkf chg = int(round(chargedict[ionname],
>>> 0))KeyError: 'C'*
>>>
>>> What would KeyError:'C' mean?
>>> Any help here would be nice.
>>> Thank you
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>>>
>>
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Received on Thu Jun 23 2016 - 15:00:03 PDT
