/home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba n_dec 21 Wed Jul 22 03:10:02 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for na and prot molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba /home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba /home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba /home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba /home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 3.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 3.2 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... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 412 786 na-prot_1001.pdb Sterical clashes 0.52417302799 Contacts, str_name: 1 394 781 na-prot_1005.pdb Sterical clashes 0.504481434059 Contacts, str_name: 2 435 762 na-prot_1003.pdb Sterical clashes 0.570866141732 Contacts, str_name: 3 380 758 na-prot_1002.pdb Sterical clashes 0.501319261214 Contacts, str_name: 4 409 772 na-prot_1004.pdb Sterical clashes 0.529792746114 Contacts, str_name: 5 427 799 na-prot_1000.pdb Sterical clashes 0.534418022528 There are 0.527508438939 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... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 434 816 na-prot_1001.pdb Sterical clashes 0.531862745098 Contacts, str_name: 1 382 799 na-prot_1005.pdb Sterical clashes 0.478097622028 Contacts, str_name: 2 395 748 na-prot_1003.pdb Sterical clashes 0.52807486631 Contacts, str_name: 3 386 728 na-prot_1002.pdb Sterical clashes 0.53021978022 Contacts, str_name: 4 376 765 na-prot_1004.pdb Sterical clashes 0.491503267974 Contacts, str_name: 5 431 777 na-prot_1000.pdb Sterical clashes 0.554697554698 Working directory is prot-na_15 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 392 743 na-prot_1001.pdb Sterical clashes 0.527590847914 Contacts, str_name: 1 349 707 na-prot_1005.pdb Sterical clashes 0.493635077793 Contacts, str_name: 2 396 780 na-prot_1003.pdb Sterical clashes 0.507692307692 Contacts, str_name: 3 423 775 na-prot_1002.pdb Sterical clashes 0.545806451613 Contacts, str_name: 4 368 721 na-prot_1004.pdb Sterical clashes 0.51040221914 Contacts, str_name: 5 337 668 na-prot_1000.pdb Sterical clashes 0.504491017964 Working directory is prot-na_20 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 275 561 na-prot_1001.pdb Sterical clashes 0.490196078431 Contacts, str_name: 1 248 540 na-prot_1005.pdb Sterical clashes 0.459259259259 Contacts, str_name: 2 233 522 na-prot_1003.pdb Sterical clashes 0.446360153257 Contacts, str_name: 3 275 600 na-prot_1002.pdb Sterical clashes 0.458333333333 Contacts, str_name: 4 214 492 na-prot_1004.pdb Sterical clashes 0.434959349593 Contacts, str_name: 5 294 616 na-prot_1000.pdb Sterical clashes 0.477272727273 Working directory is prot-na_25 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 93 252 na-prot_1001.pdb Sterical clashes 0.369047619048 Contacts, str_name: 1 89 250 na-prot_1005.pdb Sterical clashes 0.356 Contacts, str_name: 2 104 288 na-prot_1003.pdb Sterical clashes 0.361111111111 Contacts, str_name: 3 123 325 na-prot_1002.pdb Sterical clashes 0.378461538462 Contacts, str_name: 4 108 277 na-prot_1004.pdb Sterical clashes 0.389891696751 Contacts, str_name: 5 142 356 na-prot_1000.pdb Sterical clashes 0.398876404494 Working directory is prot-na_30 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 92 295 na-prot_1001.pdb Sterical clashes 0.31186440678 Contacts, str_name: 1 38 131 na-prot_1005.pdb Sterical clashes 0.290076335878 Contacts, str_name: 2 36 158 na-prot_1003.pdb Sterical clashes 0.227848101266 Contacts, str_name: 3 61 212 na-prot_1002.pdb Sterical clashes 0.287735849057 Contacts, str_name: 4 46 180 na-prot_1004.pdb Sterical clashes 0.255555555556 Contacts, str_name: 5 91 247 na-prot_1000.pdb Sterical clashes 0.368421052632 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... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 292 676 na-prot_1001.pdb Sterical clashes 0.431952662722 Contacts, str_name: 1 339 686 na-prot_1005.pdb Sterical clashes 0.49416909621 Contacts, str_name: 2 304 672 na-prot_1003.pdb Sterical clashes 0.452380952381 Contacts, str_name: 3 359 770 na-prot_1002.pdb Sterical clashes 0.466233766234 Contacts, str_name: 4 306 674 na-prot_1004.pdb Sterical clashes 0.454005934718 Contacts, str_name: 5 351 747 na-prot_1000.pdb Sterical clashes 0.469879518072 There are 0.461436988389 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... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 7 49 na-prot_1001.pdb Sterical clashes 0.142857142857 Contacts, str_name: 1 1 24 na-prot_1005.pdb Sterical clashes 0.0416666666667 Contacts, str_name: 2 6 52 na-prot_1003.pdb Sterical clashes 0.115384615385 Contacts, str_name: 3 19 72 na-prot_1002.pdb Sterical clashes 0.263888888889 Contacts, str_name: 4 1 31 na-prot_1004.pdb Sterical clashes 0.0322580645161 Contacts, str_name: 5 5 50 na-prot_1000.pdb Sterical clashes 0.1 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 O5' DC A 1 "] ['ATOM 1 N GLU A 1 '] Wed Jul 22 04:18:08 2026 /home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/17341eda-75ae-43de-892b-ca1c12be75ba/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt