/home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878 /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878 /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878 /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878 /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878 /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878 n_dec 21 Tue May 19 15:36:03 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb prepare dir: prot-na_10 0 katalog cp prot-na_5/* prot-na_10 cp from 5 Make rpar... close rpar prepare dir: prot-na_15 0 katalog cp prot-na_5/* prot-na_15 cp from 5 Make rpar... close rpar prepare dir: prot-na_20 0 katalog cp prot-na_5/* prot-na_20 cp from 5 Make rpar... close rpar prepare dir: prot-na_25 0 katalog cp prot-na_5/* prot-na_25 cp from 5 Make rpar... close rpar prepare dir: prot-na_30 0 katalog cp prot-na_5/* prot-na_30 cp from 5 Make rpar... close rpar gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 246 426 prot-na_1000.pdb Sterical clashes 0.577464788732 Contacts, str_name: 1 216 400 prot-na_1001.pdb Sterical clashes 0.54 Contacts, str_name: 2 292 481 prot-na_1002.pdb Sterical clashes 0.607068607069 Contacts, str_name: 3 133 323 prot-na_1003.pdb Sterical clashes 0.411764705882 Contacts, str_name: 4 175 322 prot-na_1004.pdb Sterical clashes 0.54347826087 Contacts, str_name: 5 212 412 prot-na_1005.pdb Sterical clashes 0.514563106796 There are 0.532389911558 in the file prot-na_5 d_names: ['prot-na_10', 'prot-na_15', 'prot-na_20', 'prot-na_25', 'prot-na_30'] Working directory is prot-na_10 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 6 81 prot-na_1000.pdb Sterical clashes 0.0740740740741 Contacts, str_name: 1 1 59 prot-na_1001.pdb Sterical clashes 0.0169491525424 Contacts, str_name: 2 2 65 prot-na_1002.pdb Sterical clashes 0.0307692307692 Contacts, str_name: 3 4 80 prot-na_1003.pdb Sterical clashes 0.05 Contacts, str_name: 4 5 58 prot-na_1004.pdb Sterical clashes 0.0862068965517 Contacts, str_name: 5 7 82 prot-na_1005.pdb Sterical clashes 0.0853658536585 Generating 10000 decoys first: 1 first: 1001 first: 2001 first: 3001 first: 4001 first: 5001 first: 6001 first: 7001 first: 8001 first: 9001 first: 10001 first: 11001 first: 12001 first: 13001 first: 14001 first: 15001 first: 16001 first: 17001 first: 18001 first: 19001 big_first_l, small_first_l ['ATOM 1 N SER A 69 '] ["ATOM 1 O5' DG A 1 "] Tue May 19 16:10:03 2026 /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/8ed59801-931e-417e-87a8-776d91cc0878/prot-na_10 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt