/home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c /home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c /home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c /home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c n_dec 21 Fri May 22 03:40:03 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 Log: ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.0 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 katal/home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c /home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c og 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: 0 473 645 prot-na_1000.pdb Sterical clashes 0.733333333333 Contacts, str_name: 1 432 630 prot-na_1001.pdb Sterical clashes 0.685714285714 Contacts, str_name: 2 477 637 prot-na_1002.pdb Sterical clashes 0.748822605965 Contacts, str_name: 3 454 641 prot-na_1003.pdb Sterical clashes 0.708268330733 Contacts, str_name: 4 462 645 prot-na_1004.pdb Sterical clashes 0.716279069767 Contacts, str_name: 5 414 641 prot-na_1005.pdb Sterical clashes 0.645865834633 There are 0.706380576691 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: 0 157 324 prot-na_1000.pdb Sterical clashes 0.484567901235 Contacts, str_name: 1 42 160 prot-na_1001.pdb Sterical clashes 0.2625 Contacts, str_name: 2 126 283 prot-na_1002.pdb Sterical clashes 0.445229681979 Contacts, str_name: 3 70 241 prot-na_1003.pdb Sterical clashes 0.290456431535 Contacts, str_name: 4 86 207 prot-na_1004.pdb Sterical clashes 0.415458937198 Contacts, str_name: 5 50 160 prot-na_1005.pdb Sterical clashes 0.3125 Working directory is prot-na_15 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 13 83 prot-na_1000.pdb Sterical clashes 0.156626506024 Contacts, str_name: 1 9 76 prot-na_1001.pdb Sterical clashes 0.118421052632 Contacts, str_name: 2 12 112 prot-na_1002.pdb Sterical clashes 0.107142857143 Contacts, str_name: 3 8 71 prot-na_1003.pdb Sterical clashes 0.112676056338 Contacts, str_name: 4 3 77 prot-na_1004.pdb Sterical clashes 0.038961038961 Contacts, str_name: 5 4 62 prot-na_1005.pdb Sterical clashes 0.0645161290323 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 GLY A 161 '] ["ATOM 1 C5' DA B 1 ", "ATOM 350 C5' DT C 2 "] Fri May 22 04:15:07 2026 /home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/ed318264-4b82-4a49-abd0-634cd5ffbd0c/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {'B': []} run_gramm1::no filtering, list1.txt -> list.txt