/home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860 n_dec 21 Tue Apr 28 15:32:04 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/12967bbf-65b9-49e9-b7a4-7793b1f8a860 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860 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 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: 0 476 949 na-prot_1001.pdb Sterical clashes 0.50158061117 Contacts, str_name: 1 537 1005 na-prot_1005.pdb Sterical clashes 0.534328358209 Contacts, str_name: 2 509 982 na-prot_1003.pdb Sterical clashes 0.5183299389 Contacts, str_name: 3 523 967 na-prot_1002.pdb Sterical clashes 0.540847983454 Contacts, str_name: 4 457 918 na-prot_1004.pdb Sterical clashes 0.497821350763 Contacts, str_name: 5 526 961 na-prot_1000.pdb Sterical clashes 0.547346514048 There are 0.523375792757 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: 0 451 904 na-prot_1001.pdb Sterical clashes 0.49889380531 Contacts, str_name: 1 398 815 na-prot_1005.pdb Sterical clashes 0.488343558282 Contacts, str_name: 2 506 962 na-prot_1003.pdb Sterical clashes 0.525987525988 Contacts, str_name: 3 426 858 na-prot_1002.pdb Sterical clashes 0.496503496503 Contacts, str_name: 4 451 927 na-prot_1004.pdb Sterical clashes 0.486515641855 Contacts, str_name: 5 437 877 na-prot_1000.pdb Sterical clashes 0.498289623717 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: 0 101 278 na-prot_1001.pdb Sterical clashes 0.363309352518 Contacts, str_name: 1 261 585 na-prot_1005.pdb Sterical clashes 0.446153846154 Contacts, str_name: 2 170 398 na-prot_1003.pdb Sterical clashes 0.427135678392 Contacts, str_name: 3 106 279 na-prot_1002.pdb Sterical clashes 0.379928315412 Contacts, str_name: 4 168 390 na-prot_1004.pdb Sterical clashes 0.430769230769 Contacts, str_name: 5 170 375 na-prot_1000.pdb Sterical clashes 0.453333333333 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 35 161 na-prot_1001.pdb Sterical clashes 0.217391304348 Contacts, str_name: 1 19 107 na-prot_1005.pdb Sterical clashes 0.177570093458 Contacts, str_name: 2 45 119 na-prot_1003.pdb Sterical clashes 0.378151260504 Contacts, str_name: 3 29 105 na-prot_1002.pdb Sterical clashes 0.27619047619 Contacts, str_name: 4 28 137 na-prot_1004.pdb Sterical clashes 0.204379562044 Contacts, str_name: 5 34 132 na-prot_1000.pdb Sterical clashes 0.257575757576 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 9 62 na-prot_1001.pdb Sterical clashes 0.145161290323 Contacts, str_name: 1 31 127 na-prot_1005.pdb Sterical clashes 0.244094488189 Contacts, str_name: 2 24 81 na-prot_1003.pdb Sterical clashes 0.296296296296 Contacts, str_name: 3 9 67 na-prot_1002.pdb Sterical clashes 0.134328358209 Contacts, str_name: 4 31 115 na-prot_1004.pdb Sterical clashes 0.269565217391 Contacts, str_name: 5 5 54 na-prot_1000.pdb Sterical clashes 0.0925925925926 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 9 48 na-prot_1001.pdb Sterical clashes 0.1875 Contacts, str_name: 1 35 121 na-prot_1005.pdb Sterical clashes 0.289256198347 Contacts, str_name: 2 9 51 na-prot_1003.pdb Sterical clashes 0.176470588235 Contacts, str_name: 3 10 72 na-prot_1002.pdb Sterical clashes 0.138888888889 Contacts, str_name: 4 20 67 na-prot_1004.pdb Sterical clashes 0.298507462687 Contacts, str_name: 5 5 53 na-prot_1000.pdb Sterical clashes 0.0943396226415 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: 0 471 950 na-prot_1001.pdb Sterical clashes 0.495789473684 Contacts, str_name: 1 493 950 na-prot_1005.pdb Sterical clashes 0.518947368421 Contacts, str_name: 2 441 901 na-prot_1003.pdb Sterical clashes 0.489456159822 Contacts, str_name: 3 476 951 na-prot_1002.pdb Sterical clashes 0.500525762355 Contacts, str_name: 4 423 848 na-prot_1004.pdb Sterical clashes 0.498820754717 Contacts, str_name: 5 468 943 na-prot_1000.pdb Sterical clashes 0.496288441145 There are 0.499971326691 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 1 52 na-prot_1001.pdb Sterical clashes 0.0192307692308 Contacts, str_name: 1 3 54 na-prot_1005.pdb Sterical clashes 0.0555555555556 Contacts, str_name: 2 2 46 na-prot_1003.pdb Sterical clashes 0.0434782608696 Contacts, str_name: 3 10 70 na-prot_1002.pdb Sterical clashes 0.142857142857 Contacts, str_name: 4 3 56 na-prot_1004.pdb Sterical clashes 0.0535714285714 Contacts, str_name: 5 6 44 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' G A 1 "] ['ATOM 1 N GLY A 12 '] Tue Apr 28 16:40:22 2026 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt