/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03 n_dec 21 Mon Jul 6 08:50:02 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/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03 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 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: 0 329 639 na-prot_1001.pdb Sterical clashes 0.514866979656 Contacts, str_name: 1 328 657 na-prot_1005.pdb Sterical clashes 0.499238964992 Contacts, str_name: 2 327 664 na-prot_1003.pdb Sterical clashes 0.492469879518 Contacts, str_name: 3 338 666 na-prot_1002.pdb Sterical clashes 0.507507507508 Contacts, str_name: 4 349 624 na-prot_1004.pdb Sterical clashes 0.559294871795 Contacts, str_name: 5 344 686 na-prot_1000.pdb Sterical clashes 0.501457725948 There are 0.512472654903 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: 0 344 642 na-prot_1001.pdb Sterical clashes 0.535825545171 Contacts, str_name: 1 336 629 na-prot_1005.pdb Sterical clashes 0.534181240064 Contacts, str_name: 2 307 611 na-prot_1003.pdb Sterical clashes 0.502454991817 Contacts, str_name: 3 291 616 na-prot_1002.pdb Sterical clashes 0.472402597403 Contacts, str_name: 4 306 621 na-prot_1004.pdb Sterical clashes 0.492753623188 Contacts, str_name: 5 328 661 na-prot_1000.pdb Sterical clashes 0.49621785174 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: 0 285 604 na-prot_1001.pdb Sterical clashes 0.471854304636 Contacts, str_name: 1 288 603 na-prot_1005.pdb Sterical clashes 0.477611940299 Contacts, str_name: 2 311 615 na-prot_1003.pdb Sterical clashes 0.505691056911 Contacts, str_name: 3 259 554 na-prot_1002.pdb Sterical clashes 0.467509025271 Contacts, str_name: 4 320 666 na-prot_1004.pdb Sterical clashes 0.48048048048 Contacts, str_name: 5 316 625 na-prot_1000.pdb Sterical clashes 0.5056 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: 0 299 649 na-prot_1001.pdb Sterical clashes 0.460708782743 Contacts, str_name: 1 297 590 na-prot_1005.pdb Sterical clashes 0.503389830508 Contacts, str_name: 2 240 534 na-prot_1003.pdb Sterical clashes 0.449438202247 Contacts, str_name: 3 307 637 na-prot_1002.pdb Sterical clashes 0.481946624804 Contacts, str_name: 4 285 604 na-prot_1004.pdb Sterical clashes 0.471854304636 Contacts, str_name: 5 257 527 na-prot_1000.pdb Sterical clashes 0.487666034156 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: 0 163 358 na-prot_1001.pdb Sterical clashes 0.45530726257 Contacts, str_name: 1 238 528 na-prot_1005.pdb Sterical clashes 0.450757575758 Contacts, str_name: 2 136 370 na-prot_1003.pdb Sterical clashes 0.367567567568 Contacts, str_name: 3 192 431 na-prot_1002.pdb Sterical clashes 0.445475638051 Contacts, str_name: 4 253 483 na-prot_1004.pdb Sterical clashes 0.52380952381 Contacts, str_name: 5 183 414 na-prot_1000.pdb Sterical clashes 0.442028985507 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 81 210 na-prot_1001.pdb Sterical clashes 0.385714285714 Contacts, str_name: 1 173 361 na-prot_1005.pdb Sterical clashes 0.479224376731 Contacts, str_name: 2 111 247 na-prot_1003.pdb Sterical clashes 0.449392712551 Contacts, str_name: 3 68 180 na-prot_1002.pdb Sterical clashes 0.377777777778 Contacts, str_name: 4 113 259 na-prot_1004.pdb Sterical clashes 0.436293436293 Contacts, str_name: 5 86 225 na-prot_1000.pdb Sterical clashes 0.382222222222 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: 0 271 550 na-prot_1001.pdb Sterical clashes 0.492727272727 Contacts, str_name: 1 267 574 na-prot_1005.pdb Sterical clashes 0.465156794425 Contacts, str_name: 2 257 594 na-prot_1003.pdb Sterical clashes 0.43265993266 Contacts, str_name: 3 284 564 na-prot_1002.pdb Sterical clashes 0.503546099291 Contacts, str_name: 4 212 496 na-prot_1004.pdb Sterical clashes 0.427419354839 Contacts, str_name: 5 245 570 na-prot_1000.pdb Sterical clashes 0.429824561404 There are 0.458555669224 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 2 37 na-prot_1001.pdb Sterical clashes 0.0540540540541 Contacts, str_name: 1 6 42 na-prot_1005.pdb Sterical clashes 0.142857142857 Contacts, str_name: 2 6 53 na-prot_1003.pdb Sterical clashes 0.11320754717 Contacts, str_name: 3 4 48 na-prot_1002.pdb Sterical clashes 0.0833333333333 Contacts, str_name: 4 12 80 na-prot_1004.pdb Sterical clashes 0.15 Contacts, str_name: 5 6 38 na-prot_1000.pdb Sterical clashes 0.157894736842 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 14 '] Mon Jul 6 09:58:05 2026 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt