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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Received on Thu Jun 23 2016 - 11:00:03 PDT
