Hi Eugene,
Change the ion_ids from 32 to 1 in the input file will fix the problem.
Kind regards,
Pengfei
> On Nov 1, 2017, at 2:14 PM, Eugene Cha <eugenekhcha.gmail.com> wrote:
>
> I'm trying to run MCPB.py using a small system with GGH and a Cu2+ ion
>
>
> I get a KeyError: 'H171' during step 1
>
> I've tried deleting H171 and I get a KeyError; 'H331' which is the previous
> H atom
>
> I feel like I'm missing something simple
>
>
> Also the standard model for some reason uses the ligand twice. Is it
> because I only have a ligand and no standard residues?
>
> I've included the files I'm using. I would really appreciate some advice
>
> Thanks
>
>
>
> Eugene
>
> *=======================Metal Site Information===================*
> * *
> ******************************************************************
> ***Selected Metal ion H171 is atom 32 in residue 2-GGH
> 2-GGH.O16 is in 2.8 Angstrom of or set bonded (in the input file) to (one
> of) these metal ions
> 2-GGH.O17 is in 2.8 Angstrom of or set bonded (in the input file) to (one
> of) these metal ions
> ***The following residues are in the Metal Site:
> Residue 2-GGH
> Residue 2-GGH
> ***The small model contains the following residues:
> [2]
> ***The large model contains the following residues:
> [2]
> ******************************************************************
> * *
> *=======================Building models==========================*
> * *
> ******************************************************************
> ***Creating the small model...
> It contains the residue 2-GGH as normal.
> Totally there are 31 atoms in the small model.
> Totally there are 145 electrons in the small model.
> ***Creating the standard model...
> It contains the residue 2-GGH as normal.
> It contains the residue 2-GGH as normal.
> Totally there are 62 atoms in the standard model.
> ***Creating the large model...
> It contains the residue 2-GGH as normal.
> Totally there are 31 atoms in the large model.
> Totally there are 145 electrons in the large model.
> Traceback (most recent call last):
> File "/home/eugenevnc/anaconda3/bin/MCPB.py", line 644, in <module>
> addred, lgchg, lgspin)
> File
> "/home/eugenevnc/anaconda3/lib/python3.5/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1901, in gene_model_files
> ionids, chargedict, lgchg, lgspin, outf, watermodel, largeopt, sqmopt)
> File
> "/home/eugenevnc/anaconda3/lib/python3.5/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1596, in build_large_model
> chargedict, IonLJParaDict, largeopt)
> File
> "/home/eugenevnc/anaconda3/lib/python3.5/site-packages/pymsmt/mol/gauio.py",
> line 294, in write_gau_mkf
> chg = int(round(chargedict[ionname], 0))
> KeyError: 'H171'
> <Cu_GGH.zip>_______________________________________________
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Received on Wed Nov 08 2017 - 07:00:02 PST
