/home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580 n_dec 21 Fri Jul 24 06:40:02 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/795a27ca-c871-4545-b7aa-ece1f90ee580 /home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580 /home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580 /home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580 /home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580 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 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: 0 249 484 na-prot_1001.pdb Sterical clashes 0.514462809917 Contacts, str_name: 1 258 488 na-prot_1005.pdb Sterical clashes 0.52868852459 Contacts, str_name: 2 266 476 na-prot_1003.pdb Sterical clashes 0.558823529412 Contacts, str_name: 3 275 497 na-prot_1002.pdb Sterical clashes 0.553319919517 Contacts, str_name: 4 232 452 na-prot_1004.pdb Sterical clashes 0.513274336283 Contacts, str_name: 5 294 495 na-prot_1000.pdb Sterical clashes 0.593939393939 There are 0.543751418943 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: 0 256 468 na-prot_1001.pdb Sterical clashes 0.547008547009 Contacts, str_name: 1 230 445 na-prot_1005.pdb Sterical clashes 0.516853932584 Contacts, str_name: 2 236 440 na-prot_1003.pdb Sterical clashes 0.536363636364 Contacts, str_name: 3 211 442 na-prot_1002.pdb Sterical clashes 0.477375565611 Contacts, str_name: 4 253 463 na-prot_1004.pdb Sterical clashes 0.546436285097 Contacts, str_name: 5 219 457 na-prot_1000.pdb Sterical clashes 0.479212253829 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: 0 222 461 na-prot_1001.pdb Sterical clashes 0.481561822126 Contacts, str_name: 1 214 427 na-prot_1005.pdb Sterical clashes 0.501170960187 Contacts, str_name: 2 207 428 na-prot_1003.pdb Sterical clashes 0.483644859813 Contacts, str_name: 3 212 433 na-prot_1002.pdb Sterical clashes 0.4896073903 Contacts, str_name: 4 239 448 na-prot_1004.pdb Sterical clashes 0.533482142857 Contacts, str_name: 5 218 439 na-prot_1000.pdb Sterical clashes 0.496583143508 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: 0 144 315 na-prot_1001.pdb Sterical clashes 0.457142857143 Contacts, str_name: 1 133 312 na-prot_1005.pdb Sterical clashes 0.426282051282 Contacts, str_name: 2 193 388 na-prot_1003.pdb Sterical clashes 0.497422680412 Contacts, str_name: 3 210 441 na-prot_1002.pdb Sterical clashes 0.47619047619 Contacts, str_name: 4 121 288 na-prot_1004.pdb Sterical clashes 0.420138888889 Contacts, str_name: 5 188 409 na-prot_1000.pdb Sterical clashes 0.459657701711 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: 0 133 290 na-prot_1001.pdb Sterical clashes 0.458620689655 Contacts, str_name: 1 117 253 na-prot_1005.pdb Sterical clashes 0.462450592885 Contacts, str_name: 2 85 182 na-prot_1003.pdb Sterical clashes 0.467032967033 Contacts, str_name: 3 63 185 na-prot_1002.pdb Sterical clashes 0.340540540541 Contacts, str_name: 4 45 143 na-prot_1004.pdb Sterical clashes 0.314685314685 Contacts, str_name: 5 76 180 na-prot_1000.pdb Sterical clashes 0.422222222222 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 45 127 na-prot_1001.pdb Sterical clashes 0.354330708661 Contacts, str_name: 1 76 212 na-prot_1005.pdb Sterical clashes 0.358490566038 Contacts, str_name: 2 43 136 na-prot_1003.pdb Sterical clashes 0.316176470588 Contacts, str_name: 3 32 101 na-prot_1002.pdb Sterical clashes 0.316831683168 Contacts, str_name: 4 26 113 na-prot_1004.pdb Sterical clashes 0.230088495575 Contacts, str_name: 5 21 109 na-prot_1000.pdb Sterical clashes 0.192660550459 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: 0 205 427 na-prot_1001.pdb Sterical clashes 0.480093676815 Contacts, str_name: 1 188 429 na-prot_1005.pdb Sterical clashes 0.438228438228 Contacts, str_name: 2 154 382 na-prot_1003.pdb Sterical clashes 0.403141361257 Contacts, str_name: 3 236 490 na-prot_1002.pdb Sterical clashes 0.481632653061 Contacts, str_name: 4 214 455 na-prot_1004.pdb Sterical clashes 0.47032967033 Contacts, str_name: 5 247 456 na-prot_1000.pdb Sterical clashes 0.541666666667 There are 0.469182077726 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 9 51 na-prot_1001.pdb Sterical clashes 0.176470588235 Contacts, str_name: 1 4 36 na-prot_1005.pdb Sterical clashes 0.111111111111 Contacts, str_name: 2 13 66 na-prot_1003.pdb Sterical clashes 0.19696969697 Contacts, str_name: 3 0 12 na-prot_1002.pdb Sterical clashes 0.0 Contacts, str_name: 4 6 64 na-prot_1004.pdb Sterical clashes 0.09375 Contacts, str_name: 5 6 63 na-prot_1000.pdb Sterical clashes 0.0952380952381 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 1 '] Fri Jul 24 07:47:39 2026 /home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/795a27ca-c871-4545-b7aa-ece1f90ee580/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt