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: 'HZ3'
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 HZ3 is atom 4018 in residue 260-LYS
21-GLU.OE2 is in 2.8 Angstrom of or set bonded (in the input file) to (one
of) these metal ions
21-GLU.O is in 2.8 Angstrom of or set bonded (in the input file) to (one
of) these metal ions
232-GLU.OE2 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 21-GLU
Residue 232-GLU
Residue 260-LYS
***The small model contains the following residues:
[21, 22, 232, 260]
***The large model contains the following residues:
[20, 21, 22, 231, 232, 233, 259, 260, 261]
******************************************************************
* *
*=======================Building models==========================*
* *
******************************************************************
***Creating the small model...
It contains the residue 21-GLU as keeping sidechain and CO group.
Creating the residue 22-ASP into NME...
It contains the residue 232-GLU as sidechain coordinated.
It contains the residue 260-LYS as sidechain coordinated.
Totally there are 53 atoms in the small model.
Totally there are 176 electrons in the small model.
***Creating the standard model...
It contains the residue 21-GLU as normal.
It contains the residue 232-GLU as normal.
It contains the residue 260-LYS as normal.
Totally there are 52 atoms in the standard model.
***Creating the large model...
Creating the residue 20-SER into ACE...
It contains the residue 21-GLU as normal.
Creating the residue 22-ASP into NME...
Creating the residue 231-LYS into ACE...
It contains the residue 232-GLU as normal.
Creating the residue 233-VAL 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 88 atoms in the large model.
Totally there are 326 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: 'HZ3'
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 07 2021 - 05:30:02 PDT
