-------------------------------------- Running PBS prologue script -------------------------------------- User and Job Data: -------------------------------------- Job ID: 830144.qb3 Username: wxx6941 Group: ullusers Date: 15-Oct-2020 19:36 Node: qb003 (66574) -------------------------------------- PBS has allocated the following nodes: qb003 A total of 1 processors on 1 nodes allocated --------------------------------------------- Check nodes and clean them of stray processes --------------------------------------------- Checking node qb003 19:36:38 Done clearing all the allocated nodes ------------------------------------------------------ Concluding PBS prologue script - 15-Oct-2020 19:36:38 ------------------------------------------------------ Loading amber/16/INTEL-140-MVAPICH2-2.0 Loading requirement: intel/14.0.2 INTEL/14.0.2 mvapich2/2.0/INTEL-14.0.2 number of cores = 1 ****************************************************************** * Welcome to use the MCPB.py program * * Version 3.0 * * Author: Pengfei Li * * Merz Research Group * * Michigan State University * * AND * * Hammes-Schiffer Research Group * * University of Illinois at Urbana-Champaign * ****************************************************************** The input file you are using is : 4ZF6.in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The following is the input variable you have: The variable ion_ids is : [7440] The variable ion_info is : [] The variable ion_mol2files is : ['FE.mol2'] The variable original_pdb is : 4ZF6_H_renum.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 : ff14SB The variable frcmod_files is : ['HEM.frcmod', '1PE.frcmod', 'EDO.frcmod'] The variable gaff is : 1 The variable group_name is : 4ZF6 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 : ['HEM.mol2', '1PE.mol2', 'EDO.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 H262 is atom 7440 in residue 463-1PE 463-1PE@OH6 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions 463-1PE@OH7 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 463-1PE Residue 463-1PE ***The small model contains the following residues: [463] ***The large model contains the following residues: [463] ****************************************************************** * * *=======================Building models==========================* * * ****************************************************************** ***Creating the small model... It contains the residue 463-1PE as normal. Totally there are 38 atoms in the small model. Totally there are 130 electrons in the small model. ***Creating the standard model... It contains the residue 463-1PE as normal. It contains the residue 463-1PE as normal. Totally there are 76 atoms in the standard model. ***Creating the large model... It contains the residue 463-1PE as normal. Totally there are 38 atoms in the large model. Totally there are 130 electrons in the large model. Traceback (most recent call last): File "/usr/local/packages/amber/16/INTEL-140-MVAPICH2-2.0//bin/MCPB.py", line 644, in addred, lgchg, lgspin) File "/usr/local/packages/amber/16/INTEL-140-MVAPICH2-2.0/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1901, in gene_model_files ionids, chargedict, lgchg, lgspin, outf, watermodel, largeopt, sqmopt) File "/usr/local/packages/amber/16/INTEL-140-MVAPICH2-2.0/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1596, in build_large_model chargedict, IonLJParaDict, largeopt) File "/usr/local/packages/amber/16/INTEL-140-MVAPICH2-2.0/lib/python2.7/site-packages/pymsmt/mol/gauio.py", line 294, in write_gau_mkf chg = int(round(chargedict[ionname], 0)) KeyError: 'H262' ------------------------------------------------------ Running PBS epilogue script - 15-Oct-2020 19:36:42 ------------------------------------------------------ Checking node qb003 (MS) Checking node qb003 ; cleared cache ; ok ------------------------------------------------------ Concluding PBS epilogue script - 15-Oct-2020 19:36:44 ------------------------------------------------------ Exit Status: 1 Job ID: 830144.qb3 Username: wxx6941 Group: ullusers Job Name: mcpb4zf6jobs1 Session Id: 66573 Resource Limits: ncpus=1,neednodes=1:ppn=1,nodes=1:ppn=1,walltime=72:00:00 Resources Used: cput=00:00:06,mem=0kb,vmem=0kb,walltime=00:00:07 Queue Used: single Account String: loni_efe_12 Node: qb003 Process id: 67243 ------------------------------------------------------