/home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73 n_dec 21 Wed Apr 29 17:00:04 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/96b18956-77ac-407c-a955-1774e79def73 /home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73 /home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73 /home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73 /home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73 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 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: 0 359 688 na-prot_1001.pdb Sterical clashes 0.521802325581 Contacts, str_name: 1 365 713 na-prot_1005.pdb Sterical clashes 0.511921458626 Contacts, str_name: 2 349 678 na-prot_1003.pdb Sterical clashes 0.514749262537 Contacts, str_name: 3 335 725 na-prot_1002.pdb Sterical clashes 0.462068965517 Contacts, str_name: 4 373 741 na-prot_1004.pdb Sterical clashes 0.503373819163 Contacts, str_name: 5 385 735 na-prot_1000.pdb Sterical clashes 0.52380952381 There are 0.506287559206 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: 0 316 698 na-prot_1001.pdb Sterical clashes 0.452722063037 Contacts, str_name: 1 348 748 na-prot_1005.pdb Sterical clashes 0.465240641711 Contacts, str_name: 2 320 689 na-prot_1003.pdb Sterical clashes 0.464441219158 Contacts, str_name: 3 349 731 na-prot_1002.pdb Sterical clashes 0.477428180575 Contacts, str_name: 4 349 725 na-prot_1004.pdb Sterical clashes 0.481379310345 Contacts, str_name: 5 347 728 na-prot_1000.pdb Sterical clashes 0.476648351648 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: 0 326 658 na-prot_1001.pdb Sterical clashes 0.495440729483 Contacts, str_name: 1 236 569 na-prot_1005.pdb Sterical clashes 0.414762741652 Contacts, str_name: 2 251 568 na-prot_1003.pdb Sterical clashes 0.441901408451 Contacts, str_name: 3 218 499 na-prot_1002.pdb Sterical clashes 0.436873747495 Contacts, str_name: 4 323 670 na-prot_1004.pdb Sterical clashes 0.482089552239 Contacts, str_name: 5 277 603 na-prot_1000.pdb Sterical clashes 0.459369817579 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: 0 153 338 na-prot_1001.pdb Sterical clashes 0.452662721893 Contacts, str_name: 1 236 527 na-prot_1005.pdb Sterical clashes 0.447817836812 Contacts, str_name: 2 196 500 na-prot_1003.pdb Sterical clashes 0.392 Contacts, str_name: 3 160 384 na-prot_1002.pdb Sterical clashes 0.416666666667 Contacts, str_name: 4 247 523 na-prot_1004.pdb Sterical clashes 0.472275334608 Contacts, str_name: 5 169 386 na-prot_1000.pdb Sterical clashes 0.437823834197 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 14 91 na-prot_1001.pdb Sterical clashes 0.153846153846 Contacts, str_name: 1 46 156 na-prot_1005.pdb Sterical clashes 0.294871794872 Contacts, str_name: 2 36 157 na-prot_1003.pdb Sterical clashes 0.229299363057 Contacts, str_name: 3 45 154 na-prot_1002.pdb Sterical clashes 0.292207792208 Contacts, str_name: 4 96 236 na-prot_1004.pdb Sterical clashes 0.406779661017 Contacts, str_name: 5 38 163 na-prot_1000.pdb Sterical clashes 0.233128834356 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 14 85 na-prot_1001.pdb Sterical clashes 0.164705882353 Contacts, str_name: 1 36 129 na-prot_1005.pdb Sterical clashes 0.279069767442 Contacts, str_name: 2 37 127 na-prot_1003.pdb Sterical clashes 0.291338582677 Contacts, str_name: 3 49 135 na-prot_1002.pdb Sterical clashes 0.362962962963 Contacts, str_name: 4 26 89 na-prot_1004.pdb Sterical clashes 0.292134831461 Contacts, str_name: 5 24 91 na-prot_1000.pdb Sterical clashes 0.263736263736 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: 0 333 704 na-prot_1001.pdb Sterical clashes 0.473011363636 Contacts, str_name: 1 285 599 na-prot_1005.pdb Sterical clashes 0.475792988314 Contacts, str_name: 2 298 647 na-prot_1003.pdb Sterical clashes 0.460587326121 Contacts, str_name: 3 293 652 na-prot_1002.pdb Sterical clashes 0.449386503067 Contacts, str_name: 4 294 596 na-prot_1004.pdb Sterical clashes 0.493288590604 Contacts, str_name: 5 336 662 na-prot_1000.pdb Sterical clashes 0.507552870091 There are 0.476603273639 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 13 80 na-prot_1001.pdb Sterical clashes 0.1625 Contacts, str_name: 1 5 49 na-prot_1005.pdb Sterical clashes 0.102040816327 Contacts, str_name: 2 2 59 na-prot_1003.pdb Sterical clashes 0.0338983050847 Contacts, str_name: 3 8 61 na-prot_1002.pdb Sterical clashes 0.131147540984 Contacts, str_name: 4 5 60 na-prot_1004.pdb Sterical clashes 0.0833333333333 Contacts, str_name: 5 3 33 na-prot_1000.pdb Sterical clashes 0.0909090909091 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 SER A 69 '] Wed Apr 29 18:07:55 2026 /home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/96b18956-77ac-407c-a955-1774e79def73/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt