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'
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Received on Wed Nov 01 2017 - 12:30:02 PDT
