Hi Sabrine,
Based on the files you sent to my email, I guess you want to parameterize a dizinc metal site (but not all the protonation states of the metal site residues are correct, you should fix this issue before performing MCPB.py modeling).
The error you mentioned was because that the ion_ids variable you set in the MCPB.py input file does not corresponds to a metal ion but corresponds to an atom in an amino acid. Your system has a dizinc center, so you should put the Atom IDs of the two zinc ions after the ion_ids variable. Please check the AMBER manual for the usage of the ion_ids variable in MCPB.py.
Pengfei
> On Jun 7, 2021, at 6:59 AM, sabrine kh <sabrine.khelifa.gmail.com> wrote:
>
> WhiIe i was trying to build bonded model for ligand binding metalloprotein
> with MCPB.py with zinc ions, I got an error.
> I run the following command "MCPB.py -i 6ye2.in -s 1" and I got the
> following error:
> chg = int(round(chargedict[ionname], 0))
> KeyError: 'HZ2'
> How can I solve this?
> Thank you
>
>
> this is 6ye2.in input file:
> original_pdb 6ye2_fixed_H.pdb
> group_name 6ye2
> cut_off 2.8
> ion_ids 4018
> ion_mol2files 6ye2_ZN.mol2
> naa_mol2files 6ye2_ligand.mol2 6ye2_WAT.mol2
> frcmod_files 6ye2_ligand.frcmod
> large_opt 1
>
>
>
> The terminal Output:
> ******************************************************************
> * Welcome to use the MCPB.py program *
> * Version 7.0 *
> * Author: Pengfei Li *
> * Merz Research Group *
> * Michigan State University *
> * AND *
> * Hammes-Schiffer Research Group *
> * Yale University *
> * AND *
> * Li Research Group *
> * Loyola University Chicago *
> ******************************************************************
> The input file you are using is : 6ye2.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> The following is the input variable you have:
> The variable ion_ids is : [4018]
> The variable ion_info is : []
> The variable ion_mol2files is : ['6ye2_ZN.mol2']
> The variable original_pdb is : 6ye2_fixed_H.pdb
> The variable add_bonded_pairs is : []
> The variable add_redcrd is : 0
> The variable additional_resids is : []
> The variable anglefc_avg is : 0
> The variable bondfc_avg is : 0
> The variable chgfix_resids is : []
> The variable cut_off is : 2.8
> The variable force_field is : ff19SB
> The variable frcmod_files is : ['6ye2_ligand.frcmod']
> The variable gaff is : 1
> The variable group_name is : 6ye2
> The variable ion_paraset is : 12_6 (Only for the ions using the nonbonded
> model).
> The variable large_opt is : 1
> The variable lgmodel_chg is : -99
> The variable lgmodel_spin is : -99
> -99 means program will assign a charge automatically.
> The variable naa_mol2files is : ['6ye2_ligand.mol2', '6ye2_WAT.mol2']
> The variable scale_factor is : 1.0
> ATTENTION: This is the scale factor of frequency. The
> force constants will be scaled by multiplying the square
> of scale_factor.
> The variable smmodel_chg is : -99
> The variable smmodel_spin is : -99
> -99 means program will assign a charge automatically.
> The variable software_version is : gau
> The variable sqm_opt is : 0
> The variable water_model is : OPC
> The variable xstru is : 0
> ******************************************************************
> * *
> *=======================Metal Site Information===================*
> * *
> ******************************************************************
> ***Selected Metal ion HZ2 is atom 4018 in residue 260-LYS
> 230-SER.OG is in 2.8 Angstrom of or set bonded (in the input file) to (one
> of) these metal ions
> 260-LYS.NZ 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 230-SER
> Residue 260-LYS
> ***The small model contains the following residues:
> [230, 260]
> ***The large model contains the following residues:
> [229, 230, 231, 259, 260, 261]
> ******************************************************************
> * *
> *=======================Building models==========================*
> * *
> ******************************************************************
> ***Creating the small model...
> It contains the residue 230-SER as sidechain coordinated.
> It contains the residue 260-LYS as sidechain coordinated.
> Totally there are 29 atoms in the small model.
> Totally there are 76 electrons in the small model.
> ***Creating the standard model...
> It contains the residue 230-SER as normal.
> It contains the residue 260-LYS as normal.
> Totally there are 33 atoms in the standard model.
> ***Creating the large model...
> Creating the residue 229-PRO into ACE...
> It contains the residue 230-SER as normal.
> Creating the residue 231-LYS into NME...
> Creating the residue 259-GLY into ACE...
> It contains the residue 260-LYS as normal.
> Creating the residue 261-TYR into NME...
> Totally there are 57 atoms in the large model.
> Totally there are 196 electrons in the large model.
> Traceback (most recent call last):
> File "/home/ubuntu/SMproject/amber20/bin/MCPB.py", line 651, in <module>
> gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
> File
> "/home/ubuntu/SMproject/amber20/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1909, in gene_model_files
> build_large_model(mol, reslist, lmsresids, lmsresace, lmsresnme,
> lmsresgly,
> File
> "/home/ubuntu/SMproject/amber20/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py",
> line 1603, in build_large_model
> write_gau_mkf(outf, gmkf, lgchg, SpinNum, gatms, ionnames,
> File
> "/home/ubuntu/SMproject/amber20/lib/python3.8/site-packages/pymsmt/mol/gauio.py",
> line 286, in write_gau_mkf
> chg = int(round(chargedict[ionname], 0))
> KeyError: 'HZ2'
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Received on Tue Jun 08 2021 - 19:30:02 PDT
