Simulating a metallo-protein Apo form

[saraujo2023]

Hi, How do I prepare a metalloprotein system in Apo form? It is a system with two proteins, and zinc coordinates the site. I need to learn how to fix this error in the preparation.

=======================Building models==========================*

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  Creating the small model... It contains the residue 4-THR as keeping sidechain and CO group. Creating the residue 5-VAL into NME... Totally there are 19 atoms in the small model. Totally there are 64 electrons in the small model. Creating the standard model... It contains the residue 4-THR as normal. It contains the residue 5-VAL as normal. Totally there are 30 atoms in the standard model. ***Creating the large model... Creating the residue 3-ARG into ACE... It contains the residue 4-THR as normal. It contains the residue 5-VAL as normal. Creating the residue 6-ARG into NME... Totally there are 42 atoms in the large model. Totally there are 148 electrons in the large model. Traceback (most recent call last): File "/opt/amber/amber22/bin/MCPB.py", line 651, in gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice, File "/opt/amber/amber22/lib/python3.12/site-packages/pymsmt/mcpb/gene_model_files.py", line 1909, in gene_model_files build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme, lmsresgly, File "/opt/amber/amber22/lib/python3.12/site-packages/pymsmt/mcpb/gene_model_files.py", line 1603, in build_large_model write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames, File "/opt/amber/amber22/lib/python3.12/site-packages/pymsmt/mol/gauio.py", line 286, in write_gau_mkf chg = int(round(chargedict[ionname], 0))

  
  KeyError: 'C'

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Can I accomplish this using Colab? Also, is it essential to create this small system for the Apo form?

I want to express my sincere gratitude in advance for any guidance.