/home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472 n_dec 21 Mon Jul 27 05:30:02 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\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 Log: ['\n', '*** ERROR: for prot and na molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for pro/home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472 /home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472 /home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472 /home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472 /home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472 t and na molecules the 3.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.9 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: 0 710 1025 prot-na_1000.pdb Sterical clashes 0.692682926829 Contacts, str_name: 1 723 1015 prot-na_1001.pdb Sterical clashes 0.712315270936 Contacts, str_name: 2 621 878 prot-na_1002.pdb Sterical clashes 0.70728929385 Contacts, str_name: 3 684 935 prot-na_1003.pdb Sterical clashes 0.731550802139 Contacts, str_name: 4 688 963 prot-na_1004.pdb Sterical clashes 0.714434060228 Contacts, str_name: 5 750 1029 prot-na_1005.pdb Sterical clashes 0.728862973761 There are 0.714522554624 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: 0 716 1018 prot-na_1000.pdb Sterical clashes 0.703339882122 Contacts, str_name: 1 650 960 prot-na_1001.pdb Sterical clashes 0.677083333333 Contacts, str_name: 2 641 927 prot-na_1002.pdb Sterical clashes 0.691477885653 Contacts, str_name: 3 711 1016 prot-na_1003.pdb Sterical clashes 0.699803149606 Contacts, str_name: 4 680 1010 prot-na_1004.pdb Sterical clashes 0.673267326733 Contacts, str_name: 5 654 930 prot-na_1005.pdb Sterical clashes 0.703225806452 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: 0 666 973 prot-na_1000.pdb Sterical clashes 0.684480986639 Contacts, str_name: 1 660 947 prot-na_1001.pdb Sterical clashes 0.696937697994 Contacts, str_name: 2 683 930 prot-na_1002.pdb Sterical clashes 0.734408602151 Contacts, str_name: 3 690 971 prot-na_1003.pdb Sterical clashes 0.710607621009 Contacts, str_name: 4 699 974 prot-na_1004.pdb Sterical clashes 0.717659137577 Contacts, str_name: 5 551 806 prot-na_1005.pdb Sterical clashes 0.683622828784 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: 0 659 927 prot-na_1000.pdb Sterical clashes 0.710895361381 Contacts, str_name: 1 641 915 prot-na_1001.pdb Sterical clashes 0.700546448087 Contacts, str_name: 2 676 969 prot-na_1002.pdb Sterical clashes 0.697626418989 Contacts, str_name: 3 565 887 prot-na_1003.pdb Sterical clashes 0.636978579481 Contacts, str_name: 4 519 818 prot-na_1004.pdb Sterical clashes 0.634474327628 Contacts, str_name: 5 671 956 prot-na_1005.pdb Sterical clashes 0.701882845188 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: 0 549 860 prot-na_1000.pdb Sterical clashes 0.638372093023 Contacts, str_name: 1 408 601 prot-na_1001.pdb Sterical clashes 0.678868552413 Contacts, str_name: 2 409 606 prot-na_1002.pdb Sterical clashes 0.674917491749 Contacts, str_name: 3 517 754 prot-na_1003.pdb Sterical clashes 0.685676392573 Contacts, str_name: 4 515 787 prot-na_1004.pdb Sterical clashes 0.654383735705 Contacts, str_name: 5 587 861 prot-na_1005.pdb Sterical clashes 0.681765389082 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: 0 543 868 prot-na_1000.pdb Sterical clashes 0.625576036866 Contacts, str_name: 1 386 584 prot-na_1001.pdb Sterical clashes 0.66095890411 Contacts, str_name: 2 446 686 prot-na_1002.pdb Sterical clashes 0.650145772595 Contacts, str_name: 3 520 760 prot-na_1003.pdb Sterical clashes 0.684210526316 Contacts, str_name: 4 533 868 prot-na_1004.pdb Sterical clashes 0.614055299539 Contacts, str_name: 5 485 828 prot-na_1005.pdb Sterical clashes 0.585748792271 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: 0 571 834 prot-na_1000.pdb Sterical clashes 0.684652278177 Contacts, str_name: 1 696 975 prot-na_1001.pdb Sterical clashes 0.713846153846 Contacts, str_name: 2 639 916 prot-na_1002.pdb Sterical clashes 0.697598253275 Contacts, str_name: 3 621 939 prot-na_1003.pdb Sterical clashes 0.661341853035 Contacts, str_name: 4 568 904 prot-na_1004.pdb Sterical clashes 0.628318584071 Contacts, str_name: 5 652 995 prot-na_1005.pdb Sterical clashes 0.65527638191 There are 0.673505584052 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 21 82 prot-na_1000.pdb Sterical clashes 0.256097560976 Contacts, str_name: 1 11 99 prot-na_1001.pdb Sterical clashes 0.111111111111 Contacts, str_name: 2 13 82 prot-na_1002.pdb Sterical clashes 0.158536585366 Contacts, str_name: 3 3 33 prot-na_1003.pdb Sterical clashes 0.0909090909091 Contacts, str_name: 4 3 40 prot-na_1004.pdb Sterical clashes 0.075 Contacts, str_name: 5 5 61 prot-na_1005.pdb Sterical clashes 0.0819672131148 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 24 '] ["ATOM 1 O5' DC A 1 "] Mon Jul 27 06:39:12 2026 /home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/e0f14ade-f550-48bc-bcbb-a97c4e22d472/prot-na_10 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt