/home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe n_dec 21 Tue Apr 28 12:32:04 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/3d411e53-5cb9-4307-9924-83be5dc86afe /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe 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 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 1029 1598 prot-na_1000.pdb Sterical clashes 0.64392991239 Contacts, str_name: 1 1009 1576 prot-na_1001.pdb Sterical clashes 0.640228426396 Contacts, str_name: 2 968 1477 prot-na_1002.pdb Sterical clashes 0.65538253216 Contacts, str_name: 3 1033 1587 prot-na_1003.pdb Sterical clashes 0.650913673598 Contacts, str_name: 4 1074 1549 prot-na_1004.pdb Sterical clashes 0.693350548741 Contacts, str_name: 5 975 1538 prot-na_1005.pdb Sterical clashes 0.633940182055 There are 0.65295754589 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: 0 904 1517 prot-na_1000.pdb Sterical clashes 0.595912986157 Contacts, str_name: 1 968 1506 prot-na_1001.pdb Sterical clashes 0.642762284197 Contacts, str_name: 2 1003 1571 prot-na_1002.pdb Sterical clashes 0.638446849141 Contacts, str_name: 3 957 1485 prot-na_1003.pdb Sterical clashes 0.644444444444 Contacts, str_name: 4 959 1528 prot-na_1004.pdb Sterical clashes 0.627617801047 Contacts, str_name: 5 998 1557 prot-na_1005.pdb Sterical clashes 0.640976236352 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: 0 949 1502 prot-na_1000.pdb Sterical clashes 0.631824234354 Contacts, str_name: 1 1017 1595 prot-na_1001.pdb Sterical clashes 0.637617554859 Contacts, str_name: 2 1022 1577 prot-na_1002.pdb Sterical clashes 0.648065948003 Contacts, str_name: 3 858 1364 prot-na_1003.pdb Sterical clashes 0.629032258065 Contacts, str_name: 4 791 1431 prot-na_1004.pdb Sterical clashes 0.552760307477 Contacts, str_name: 5 911 1471 prot-na_1005.pdb Sterical clashes 0.619306594154 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: 0 738 1357 prot-na_1000.pdb Sterical clashes 0.543846720707 Contacts, str_name: 1 849 1417 prot-na_1001.pdb Sterical clashes 0.599153140438 Contacts, str_name: 2 479 922 prot-na_1002.pdb Sterical clashes 0.519522776573 Contacts, str_name: 3 854 1473 prot-na_1003.pdb Sterical clashes 0.579769178547 Contacts, str_name: 4 701 1194 prot-na_1004.pdb Sterical clashes 0.587102177554 Contacts, str_name: 5 784 1327 prot-na_1005.pdb Sterical clashes 0.590806330068 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: 0 132 337 prot-na_1000.pdb Sterical clashes 0.391691394659 Contacts, str_name: 1 291 600 prot-na_1001.pdb Sterical clashes 0.485 Contacts, str_name: 2 265 642 prot-na_1002.pdb Sterical clashes 0.41277258567 Contacts, str_name: 3 187 514 prot-na_1003.pdb Sterical clashes 0.363813229572 Contacts, str_name: 4 109 246 prot-na_1004.pdb Sterical clashes 0.443089430894 Contacts, str_name: 5 528 996 prot-na_1005.pdb Sterical clashes 0.530120481928 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: 0 153 400 prot-na_1000.pdb Sterical clashes 0.3825 Contacts, str_name: 1 75 218 prot-na_1001.pdb Sterical clashes 0.344036697248 Contacts, str_name: 2 74 266 prot-na_1002.pdb Sterical clashes 0.278195488722 Contacts, str_name: 3 60 151 prot-na_1003.pdb Sterical clashes 0.397350993377 Contacts, str_name: 4 23 120 prot-na_1004.pdb Sterical clashes 0.191666666667 Contacts, str_name: 5 32 79 prot-na_1005.pdb Sterical clashes 0.405063291139 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: 0 961 1574 prot-na_1000.pdb Sterical clashes 0.610546378653 Contacts, str_name: 1 1013 1536 prot-na_1001.pdb Sterical clashes 0.659505208333 Contacts, str_name: 2 828 1493 prot-na_1002.pdb Sterical clashes 0.554588077696 Contacts, str_name: 3 1035 1589 prot-na_1003.pdb Sterical clashes 0.651353052234 Contacts, str_name: 4 977 1548 prot-na_1004.pdb Sterical clashes 0.631136950904 Contacts, str_name: 5 888 1492 prot-na_1005.pdb Sterical clashes 0.595174262735 There are 0.617050655093 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 15 103 prot-na_1000.pdb Sterical clashes 0.145631067961 Contacts, str_name: 1 7 78 prot-na_1001.pdb Sterical clashes 0.0897435897436 Contacts, str_name: 2 14 81 prot-na_1002.pdb Sterical clashes 0.172839506173 Contacts, str_name: 3 8 76 prot-na_1003.pdb Sterical clashes 0.105263157895 Contacts, str_name: 4 10 98 prot-na_1004.pdb Sterical clashes 0.102040816327 Contacts, str_name: 5 39 116 prot-na_1005.pdb Sterical clashes 0.336206896552 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 0 58 prot-na_1000.pdb Sterical clashes 0.0 Contacts, str_name: 1 2 33 prot-na_1001.pdb Sterical clashes 0.0606060606061 Contacts, str_name: 2 0 22 prot-na_1002.pdb Sterical clashes 0.0 Contacts, str_name: 3 1 34 prot-na_1003.pdb Sterical clashes 0.0294117647059 Contacts, str_name: 4 0 38 prot-na_1004.pdb Sterical clashes 0.0 Contacts, str_name: 5 1 26 prot-na_1005.pdb Sterical clashes 0.0384615384615 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 LEU A1011 ', 'ATOM 3707 N LEU B1011 '] ['ATOM 33 P G C 1 '] Tue Apr 28 13:43:59 2026 /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {'C': []} run_gramm1::no filtering, list1.txt -> list.txt