/home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2 n_dec 21 Wed Apr 29 10:29:04 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/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2 /home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2 /home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2 /home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2 /home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2 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: 0 371 757 na-prot_1001.pdb Sterical clashes 0.490092470277 Contacts, str_name: 1 385 766 na-prot_1005.pdb Sterical clashes 0.502610966057 Contacts, str_name: 2 364 729 na-prot_1003.pdb Sterical clashes 0.499314128944 Contacts, str_name: 3 374 711 na-prot_1002.pdb Sterical clashes 0.526019690577 Contacts, str_name: 4 371 740 na-prot_1004.pdb Sterical clashes 0.501351351351 Contacts, str_name: 5 409 787 na-prot_1000.pdb Sterical clashes 0.519695044473 There are 0.506513941947 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: 0 335 656 na-prot_1001.pdb Sterical clashes 0.510670731707 Contacts, str_name: 1 358 729 na-prot_1005.pdb Sterical clashes 0.491083676269 Contacts, str_name: 2 348 727 na-prot_1003.pdb Sterical clashes 0.478679504814 Contacts, str_name: 3 323 679 na-prot_1002.pdb Sterical clashes 0.475699558174 Contacts, str_name: 4 379 758 na-prot_1004.pdb Sterical clashes 0.5 Contacts, str_name: 5 381 728 na-prot_1000.pdb Sterical clashes 0.523351648352 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: 0 351 703 na-prot_1001.pdb Sterical clashes 0.499288762447 Contacts, str_name: 1 326 692 na-prot_1005.pdb Sterical clashes 0.471098265896 Contacts, str_name: 2 336 671 na-prot_1003.pdb Sterical clashes 0.500745156483 Contacts, str_name: 3 324 700 na-prot_1002.pdb Sterical clashes 0.462857142857 Contacts, str_name: 4 290 651 na-prot_1004.pdb Sterical clashes 0.445468509985 Contacts, str_name: 5 314 685 na-prot_1000.pdb Sterical clashes 0.458394160584 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: 0 242 516 na-prot_1001.pdb Sterical clashes 0.468992248062 Contacts, str_name: 1 313 657 na-prot_1005.pdb Sterical clashes 0.476407914764 Contacts, str_name: 2 232 520 na-prot_1003.pdb Sterical clashes 0.446153846154 Contacts, str_name: 3 340 686 na-prot_1002.pdb Sterical clashes 0.495626822157 Contacts, str_name: 4 226 488 na-prot_1004.pdb Sterical clashes 0.463114754098 Contacts, str_name: 5 222 509 na-prot_1000.pdb Sterical clashes 0.436149312377 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 60 191 na-prot_1001.pdb Sterical clashes 0.314136125654 Contacts, str_name: 1 89 260 na-prot_1005.pdb Sterical clashes 0.342307692308 Contacts, str_name: 2 78 207 na-prot_1003.pdb Sterical clashes 0.376811594203 Contacts, str_name: 3 122 251 na-prot_1002.pdb Sterical clashes 0.486055776892 Contacts, str_name: 4 109 263 na-prot_1004.pdb Sterical clashes 0.414448669202 Contacts, str_name: 5 65 213 na-prot_1000.pdb Sterical clashes 0.305164319249 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 30 97 na-prot_1001.pdb Sterical clashes 0.309278350515 Contacts, str_name: 1 54 157 na-prot_1005.pdb Sterical clashes 0.343949044586 Contacts, str_name: 2 51 154 na-prot_1003.pdb Sterical clashes 0.331168831169 Contacts, str_name: 3 39 114 na-prot_1002.pdb Sterical clashes 0.342105263158 Contacts, str_name: 4 44 152 na-prot_1004.pdb Sterical clashes 0.289473684211 Contacts, str_name: 5 35 115 na-prot_1000.pdb Sterical clashes 0.304347826087 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: 0 293 707 na-prot_1001.pdb Sterical clashes 0.414427157001 Contacts, str_name: 1 359 713 na-prot_1005.pdb Sterical clashes 0.50350631136 Contacts, str_name: 2 371 767 na-prot_1003.pdb Sterical clashes 0.48370273794 Contacts, str_name: 3 353 736 na-prot_1002.pdb Sterical clashes 0.479619565217 Contacts, str_name: 4 356 717 na-prot_1004.pdb Sterical clashes 0.496513249651 Contacts, str_name: 5 334 707 na-prot_1000.pdb Sterical clashes 0.472418670438 There are 0.475031281935 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 45 na-prot_1001.pdb Sterical clashes 0.2 Contacts, str_name: 1 3 52 na-prot_1005.pdb Sterical clashes 0.0576923076923 Contacts, str_name: 2 0 13 na-prot_1003.pdb Sterical clashes 0.0 Contacts, str_name: 3 1 29 na-prot_1002.pdb Sterical clashes 0.0344827586207 Contacts, str_name: 4 5 35 na-prot_1004.pdb Sterical clashes 0.142857142857 Contacts, str_name: 5 12 70 na-prot_1000.pdb Sterical clashes 0.171428571429 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 11:37:10 2026 /home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/86f6fa93-7be4-4e99-8f2a-ddfca4cdd3f2/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt