/home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4 n_dec 21 Thu Jun 4 07:38:03 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 Log: ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4 /home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4 /home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4 /home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4 /home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4 n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.0 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 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: 0 465 711 prot-na_1000.pdb Sterical clashes 0.654008438819 Contacts, str_name: 1 422 708 prot-na_1001.pdb Sterical clashes 0.59604519774 Contacts, str_name: 2 443 681 prot-na_1002.pdb Sterical clashes 0.650513950073 Contacts, str_name: 3 440 697 prot-na_1003.pdb Sterical clashes 0.631276901004 Contacts, str_name: 4 446 703 prot-na_1004.pdb Sterical clashes 0.634423897582 Contacts, str_name: 5 427 695 prot-na_1005.pdb Sterical clashes 0.614388489209 There are 0.630109479071 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: 0 431 696 prot-na_1000.pdb Sterical clashes 0.619252873563 Contacts, str_name: 1 440 677 prot-na_1001.pdb Sterical clashes 0.649926144756 Contacts, str_name: 2 417 690 prot-na_1002.pdb Sterical clashes 0.604347826087 Contacts, str_name: 3 408 699 prot-na_1003.pdb Sterical clashes 0.583690987124 Contacts, str_name: 4 378 658 prot-na_1004.pdb Sterical clashes 0.574468085106 Contacts, str_name: 5 404 682 prot-na_1005.pdb Sterical clashes 0.592375366569 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: 0 335 634 prot-na_1000.pdb Sterical clashes 0.528391167192 Contacts, str_name: 1 337 625 prot-na_1001.pdb Sterical clashes 0.5392 Contacts, str_name: 2 355 601 prot-na_1002.pdb Sterical clashes 0.590682196339 Contacts, str_name: 3 348 630 prot-na_1003.pdb Sterical clashes 0.552380952381 Contacts, str_name: 4 323 625 prot-na_1004.pdb Sterical clashes 0.5168 Contacts, str_name: 5 257 508 prot-na_1005.pdb Sterical clashes 0.505905511811 Working directory is prot-na_20 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: 0 172 379 prot-na_1000.pdb Sterical clashes 0.45382585752 Contacts, str_name: 1 265 527 prot-na_1001.pdb Sterical clashes 0.50284629981 Contacts, str_name: 2 197 432 prot-na_1002.pdb Sterical clashes 0.456018518519 Contacts, str_name: 3 201 413 prot-na_1003.pdb Sterical clashes 0.486682808717 Contacts, str_name: 4 111 271 prot-na_1004.pdb Sterical clashes 0.409594095941 Contacts, str_name: 5 305 609 prot-na_1005.pdb Sterical clashes 0.500821018062 Working directory is prot-na_25 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 42 127 prot-na_1000.pdb Sterical clashes 0.330708661417 Contacts, str_name: 1 131 311 prot-na_1001.pdb Sterical clashes 0.421221864952 Contacts, str_name: 2 110 291 prot-na_1002.pdb Sterical clashes 0.378006872852 Contacts, str_name: 3 76 156 prot-na_1003.pdb Sterical clashes 0.487179487179 Contacts, str_name: 4 29 131 prot-na_1004.pdb Sterical clashes 0.221374045802 Contacts, str_name: 5 68 179 prot-na_1005.pdb Sterical clashes 0.379888268156 Working directory is prot-na_30 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 25 121 prot-na_1000.pdb Sterical clashes 0.206611570248 Contacts, str_name: 1 62 156 prot-na_1001.pdb Sterical clashes 0.397435897436 Contacts, str_name: 2 9 112 prot-na_1002.pdb Sterical clashes 0.0803571428571 Contacts, str_name: 3 11 92 prot-na_1003.pdb Sterical clashes 0.119565217391 Contacts, str_name: 4 27 86 prot-na_1004.pdb Sterical clashes 0.313953488372 Contacts, str_name: 5 49 160 prot-na_1005.pdb Sterical clashes 0.30625 It is no appropriate decoys in the high resolution docking. Low resolution docking is starting! gramm scan now gramm scan now gramm scan now gramm scan now gramm scan now gramm scan now 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: 0 403 696 prot-na_1000.pdb Sterical clashes 0.579022988506 Contacts, str_name: 1 410 698 prot-na_1001.pdb Sterical clashes 0.587392550143 Contacts, str_name: 2 388 708 prot-na_1002.pdb Sterical clashes 0.54802259887 Contacts, str_name: 3 428 702 prot-na_1003.pdb Sterical clashes 0.609686609687 Contacts, str_name: 4 409 704 prot-na_1004.pdb Sterical clashes 0.580965909091 Contacts, str_name: 5 400 701 prot-na_1005.pdb Sterical clashes 0.570613409415 There are 0.579284010952 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 0 47 prot-na_1000.pdb Sterical clashes 0.0 Contacts, str_name: 1 5 71 prot-na_1001.pdb Sterical clashes 0.0704225352113 Contacts, str_name: 2 0 69 prot-na_1002.pdb Sterical clashes 0.0 Contacts, str_name: 3 19 76 prot-na_1003.pdb Sterical clashes 0.25 Contacts, str_name: 4 2 71 prot-na_1004.pdb Sterical clashes 0.0281690140845 Contacts, str_name: 5 10 73 prot-na_1005.pdb Sterical clashes 0.13698630137 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 ALA A 40 ', 'ATOM 4386 N GLY B 6 ', 'ATOM 5657 N GLY C 1 '] ["ATOM 1 O5' DG A 1 "] Thu Jun 4 09:39:18 2026 /home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/f775fcb9-c42c-47c5-8a1a-88877a6d28b4/prot-na_10 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt