****************************************************************** * Welcome to use the MCPB.py program * * Version 5.0 * * Author: Pengfei Li * * Merz Research Group * * Michigan State University * * AND * * Hammes-Schiffer Research Group * * Yale University * ****************************************************************** The input file you are using is : mcpb.in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The following is the input variable you have: The variable ion_ids is : [7756, 7757] The variable ion_info is : [] The variable ion_mol2files is : ['FE2.mol2'] The variable original_pdb is : dhad_dhiv_II-II.pdb The variable add_bonded_pairs is : [(7756, 2323), (7756, 7766), (7756, 7758), (7756, 7759), (7757, 1289), (7757, 243), (7757, 7758), (7757, 7759)] 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 : ff14SB The variable frcmod_files is : ['DHV.frcmod'] The variable gaff is : 2 The variable group_name is : 2Fe-2S_param The variable ion_paraset is : CM (Only for nonbonded model) The variable large_opt is : 0 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 : ['DHV.mol2', 'SFE.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 : g09 The variable sqm_opt is : 0 The variable water_model is : TIP3P The variable xstru is : 0 ****************************************************************** * * *=======================Metal Site Information===================* * * ****************************************************************** ***Selected Metal ion FE is atom 7756 in residue 529-FE2 ***Selected Metal ion FE is atom 7757 in residue 530-FE2 162-CYS@SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 530-FE2@FE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 531-SFE@SFE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 532-SFE@SFE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 534-DHV@O1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 17-CYS@SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 90-CYS@SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 529-FE2@FE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 162-CYS@SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 534-DHV@O1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 531-SFE@SFE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 532-SFE@SFE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 90-CYS@SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 17-CYS@SG is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 531-SFE@SFE is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 532-SFE@SFE 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 17-CYS Residue 90-CYS Residue 162-CYS Residue 529-FE2 Residue 530-FE2 Residue 531-SFE Residue 532-SFE Residue 534-DHV ***The small model contains the following residues: [17, 90, 162, 529, 530, 531, 532, 534] ***The large model contains the following residues: [16, 17, 18, 89, 90, 91, 161, 162, 163, 529, 530, 531, 532, 534] ****************************************************************** * * *=======================Building models==========================* * * ****************************************************************** ***Creating the small model... It contains the residue 17-CYS as sidechain coordinated. It contains the residue 90-CYS as sidechain coordinated. It contains the residue 162-CYS as sidechain coordinated. It contains the residue 529-FE2 as normal. It contains the residue 530-FE2 as normal. It contains the residue 531-SFE as normal. It contains the residue 532-SFE as normal. It contains the residue 534-DHV as normal. Totally there are 46 atoms in the small model. Totally there are 221 electrons in the small model. ***Creating the standard model... It contains the residue 17-CYS as normal. It contains the residue 90-CYS as normal. It contains the residue 162-CYS as normal. It contains the residue 529-FE2 as normal. It contains the residue 530-FE2 as normal. It contains the residue 531-SFE as normal. It contains the residue 532-SFE as normal. It contains the residue 534-DHV as normal. Totally there are 52 atoms in the standard model. ***Creating the large model... Creating the residue 16-PRO into ACE... It contains the residue 17-CYS as normal. Creating the residue 18-ASN into NME... Creating the residue 89-GLY into ACE... It contains the residue 90-CYS as normal. Creating the residue 91-ASP into NME... Creating the residue 161-SER into ACE... It contains the residue 162-CYS as normal. Creating the residue 163-GLY into NME... It contains the residue 529-FE2 as normal. It contains the residue 530-FE2 as normal. It contains the residue 531-SFE as normal. It contains the residue 532-SFE as normal. It contains the residue 534-DHV as normal. Totally there are 88 atoms in the large model. Totally there are 401 electrons in the large model. Traceback (most recent call last): File "/opt/amber/amber18/bin/MCPB.py", line 644, in addred, lgchg, lgspin) File "/opt/amber/amber18/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1910, in gene_model_files ionids, chargedict, lgchg, lgspin, outf, watermodel, largeopt, sqmopt) File "/opt/amber/amber18/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1604, in build_large_model chargedict, IonLJParaDict, largeopt) File "/opt/amber/amber18/lib/python3.7/site-packages/pymsmt/mol/gauio.py", line 286, in write_gau_mkf chg = int(round(chargedict[ionname], 0)) KeyError: 'FE'