/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a n_dec 21 Wed Jul 22 10:23:03 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/1a4e97f7-4e09-4089-b51a-64727243428a /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a 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: 0 494 963 na-prot_1001.pdb Sterical clashes 0.51298026999 Contacts, str_name: 1 530 964 na-prot_1005.pdb Sterical clashes 0.54979253112 Contacts, str_name: 2 544 1001 na-prot_1003.pdb Sterical clashes 0.543456543457 Contacts, str_name: 3 528 940 na-prot_1002.pdb Sterical clashes 0.56170212766 Contacts, str_name: 4 449 938 na-prot_1004.pdb Sterical clashes 0.47867803838 Contacts, str_name: 5 532 1008 na-prot_1000.pdb Sterical clashes 0.527777777778 There are 0.529064548064 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: 0 483 898 na-prot_1001.pdb Sterical clashes 0.537861915367 Contacts, str_name: 1 450 927 na-prot_1005.pdb Sterical clashes 0.485436893204 Contacts, str_name: 2 502 986 na-prot_1003.pdb Sterical clashes 0.509127789047 Contacts, str_name: 3 519 957 na-prot_1002.pdb Sterical clashes 0.542319749216 Contacts, str_name: 4 482 984 na-prot_1004.pdb Sterical clashes 0.489837398374 Contacts, str_name: 5 495 930 na-prot_1000.pdb Sterical clashes 0.532258064516 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: 0 471 931 na-prot_1001.pdb Sterical clashes 0.505907626208 Contacts, str_name: 1 414 902 na-prot_1005.pdb Sterical clashes 0.458980044346 Contacts, str_name: 2 435 924 na-prot_1003.pdb Sterical clashes 0.470779220779 Contacts, str_name: 3 427 938 na-prot_1002.pdb Sterical clashes 0.455223880597 Contacts, str_name: 4 476 923 na-prot_1004.pdb Sterical clashes 0.51570964247 Contacts, str_name: 5 417 879 na-prot_1000.pdb Sterical clashes 0.474402730375 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: 0 359 763 na-prot_1001.pdb Sterical clashes 0.470511140236 Contacts, str_name: 1 423 871 na-prot_1005.pdb Sterical clashes 0.485648679679 Contacts, str_name: 2 329 721 na-prot_1003.pdb Sterical clashes 0.456310679612 Contacts, str_name: 3 389 769 na-prot_1002.pdb Sterical clashes 0.505851755527 Contacts, str_name: 4 429 860 na-prot_1004.pdb Sterical clashes 0.498837209302 Contacts, str_name: 5 448 852 na-prot_1000.pdb Sterical clashes 0.525821596244 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: 0 274 576 na-prot_1001.pdb Sterical clashes 0.475694444444 Contacts, str_name: 1 286 645 na-prot_1005.pdb Sterical clashes 0.443410852713 Contacts, str_name: 2 189 441 na-prot_1003.pdb Sterical clashes 0.428571428571 Contacts, str_name: 3 215 475 na-prot_1002.pdb Sterical clashes 0.452631578947 Contacts, str_name: 4 264 584 na-prot_1004.pdb Sterical clashes 0.452054794521 Contacts, str_name: 5 204 461 na-prot_1000.pdb Sterical clashes 0.44251626898 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: 0 217 511 na-prot_1001.pdb Sterical clashes 0.424657534247 Contacts, str_name: 1 140 315 na-prot_1005.pdb Sterical clashes 0.444444444444 Contacts, str_name: 2 218 523 na-prot_1003.pdb Sterical clashes 0.416826003824 Contacts, str_name: 3 150 353 na-prot_1002.pdb Sterical clashes 0.42492917847 Contacts, str_name: 4 132 287 na-prot_1004.pdb Sterical clashes 0.459930313589 Contacts, str_name: 5 173 409 na-prot_1000.pdb Sterical clashes 0.422982885086 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: 0 446 922 na-prot_1001.pdb Sterical clashes 0.483731019523 Contacts, str_name: 1 419 889 na-prot_1005.pdb Sterical clashes 0.471316085489 Contacts, str_name: 2 324 725 na-prot_1003.pdb Sterical clashes 0.446896551724 Contacts, str_name: 3 421 857 na-prot_1002.pdb Sterical clashes 0.491248541424 Contacts, str_name: 4 339 770 na-prot_1004.pdb Sterical clashes 0.44025974026 Contacts, str_name: 5 353 823 na-prot_1000.pdb Sterical clashes 0.428918590522 There are 0.460395088157 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 6 80 na-prot_1001.pdb Sterical clashes 0.075 Contacts, str_name: 1 0 15 na-prot_1005.pdb Sterical clashes 0.0 Contacts, str_name: 2 9 76 na-prot_1003.pdb Sterical clashes 0.118421052632 Contacts, str_name: 3 4 46 na-prot_1002.pdb Sterical clashes 0.0869565217391 Contacts, str_name: 4 17 96 na-prot_1004.pdb Sterical clashes 0.177083333333 Contacts, str_name: 5 3 22 na-prot_1000.pdb Sterical clashes 0.136363636364 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 VAL C 14 ', 'ATOM 762 N VAL D 14 '] Wed Jul 22 11:31:25 2026 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'C': []} run_gramm1::no filtering, list1.txt -> list.txt