/home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f n_dec 21 Mon Jul 27 14:35:02 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/6a8b6219-b54a-4582-8861-18ffe22a440f /home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f /home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f /home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f /home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f 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 Log: ['\n', '*** ERROR: for na and prot molecules the 3.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 3.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 3.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 3.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 3.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 3.5 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: 0 324 640 na-prot_1001.pdb Sterical clashes 0.50625 Contacts, str_name: 1 339 618 na-prot_1005.pdb Sterical clashes 0.54854368932 Contacts, str_name: 2 375 638 na-prot_1003.pdb Sterical clashes 0.587774294671 Contacts, str_name: 3 355 651 na-prot_1002.pdb Sterical clashes 0.545314900154 Contacts, str_name: 4 341 627 na-prot_1004.pdb Sterical clashes 0.543859649123 Contacts, str_name: 5 349 604 na-prot_1000.pdb Sterical clashes 0.577814569536 There are 0.551592850467 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: 0 365 634 na-prot_1001.pdb Sterical clashes 0.57570977918 Contacts, str_name: 1 365 642 na-prot_1005.pdb Sterical clashes 0.568535825545 Contacts, str_name: 2 358 634 na-prot_1003.pdb Sterical clashes 0.564668769716 Contacts, str_name: 3 365 613 na-prot_1002.pdb Sterical clashes 0.595432300163 Contacts, str_name: 4 349 662 na-prot_1004.pdb Sterical clashes 0.527190332326 Contacts, str_name: 5 333 610 na-prot_1000.pdb Sterical clashes 0.545901639344 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: 0 331 631 na-prot_1001.pdb Sterical clashes 0.524564183835 Contacts, str_name: 1 309 570 na-prot_1005.pdb Sterical clashes 0.542105263158 Contacts, str_name: 2 327 613 na-prot_1003.pdb Sterical clashes 0.533442088091 Contacts, str_name: 3 334 609 na-prot_1002.pdb Sterical clashes 0.548440065681 Contacts, str_name: 4 323 601 na-prot_1004.pdb Sterical clashes 0.537437603993 Contacts, str_name: 5 339 642 na-prot_1000.pdb Sterical clashes 0.528037383178 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: 0 236 511 na-prot_1001.pdb Sterical clashes 0.461839530333 Contacts, str_name: 1 308 574 na-prot_1005.pdb Sterical clashes 0.536585365854 Contacts, str_name: 2 290 578 na-prot_1003.pdb Sterical clashes 0.501730103806 Contacts, str_name: 3 295 550 na-prot_1002.pdb Sterical clashes 0.536363636364 Contacts, str_name: 4 235 450 na-prot_1004.pdb Sterical clashes 0.522222222222 Contacts, str_name: 5 282 573 na-prot_1000.pdb Sterical clashes 0.492146596859 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: 0 255 544 na-prot_1001.pdb Sterical clashes 0.46875 Contacts, str_name: 1 162 351 na-prot_1005.pdb Sterical clashes 0.461538461538 Contacts, str_name: 2 144 339 na-prot_1003.pdb Sterical clashes 0.424778761062 Contacts, str_name: 3 224 499 na-prot_1002.pdb Sterical clashes 0.448897795591 Contacts, str_name: 4 228 487 na-prot_1004.pdb Sterical clashes 0.4681724846 Contacts, str_name: 5 203 451 na-prot_1000.pdb Sterical clashes 0.450110864745 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 83 252 na-prot_1001.pdb Sterical clashes 0.329365079365 Contacts, str_name: 1 60 188 na-prot_1005.pdb Sterical clashes 0.31914893617 Contacts, str_name: 2 127 311 na-prot_1003.pdb Sterical clashes 0.408360128617 Contacts, str_name: 3 146 324 na-prot_1002.pdb Sterical clashes 0.450617283951 Contacts, str_name: 4 184 403 na-prot_1004.pdb Sterical clashes 0.456575682382 Contacts, str_name: 5 173 371 na-prot_1000.pdb Sterical clashes 0.466307277628 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: 0 270 575 na-prot_1001.pdb Sterical clashes 0.469565217391 Contacts, str_name: 1 308 577 na-prot_1005.pdb Sterical clashes 0.533795493934 Contacts, str_name: 2 300 564 na-prot_1003.pdb Sterical clashes 0.531914893617 Contacts, str_name: 3 316 594 na-prot_1002.pdb Sterical clashes 0.531986531987 Contacts, str_name: 4 318 607 na-prot_1004.pdb Sterical clashes 0.523887973641 Contacts, str_name: 5 232 469 na-prot_1000.pdb Sterical clashes 0.494669509595 There are 0.514303270027 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 4 46 na-prot_1001.pdb Sterical clashes 0.0869565217391 Contacts, str_name: 1 0 21 na-prot_1005.pdb Sterical clashes 0.0 Contacts, str_name: 2 3 57 na-prot_1003.pdb Sterical clashes 0.0526315789474 Contacts, str_name: 3 4 36 na-prot_1002.pdb Sterical clashes 0.111111111111 Contacts, str_name: 4 7 62 na-prot_1004.pdb Sterical clashes 0.112903225806 Contacts, str_name: 5 5 37 na-prot_1000.pdb Sterical clashes 0.135135135135 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 GLY A 10 '] Mon Jul 27 15:43:03 2026 /home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/6a8b6219-b54a-4582-8861-18ffe22a440f/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt