/home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16 n_dec 21 Sat May 23 00:09:03 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16 /home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16 /home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16 /home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16 /home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16 n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.6 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 470 755 prot-na_1000.pdb Sterical clashes 0.622516556291 Contacts, str_name: 1 511 763 prot-na_1001.pdb Sterical clashes 0.669724770642 Contacts, str_name: 2 462 748 prot-na_1002.pdb Sterical clashes 0.617647058824 Contacts, str_name: 3 471 760 prot-na_1003.pdb Sterical clashes 0.619736842105 Contacts, str_name: 4 505 776 prot-na_1004.pdb Sterical clashes 0.650773195876 Contacts, str_name: 5 469 724 prot-na_1005.pdb Sterical clashes 0.647790055249 There are 0.638031413165 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 460 734 prot-na_1000.pdb Sterical clashes 0.626702997275 Contacts, str_name: 1 454 711 prot-na_1001.pdb Sterical clashes 0.638537271449 Contacts, str_name: 2 474 772 prot-na_1002.pdb Sterical clashes 0.613989637306 Contacts, str_name: 3 436 710 prot-na_1003.pdb Sterical clashes 0.614084507042 Contacts, str_name: 4 434 727 prot-na_1004.pdb Sterical clashes 0.596973865199 Contacts, str_name: 5 421 751 prot-na_1005.pdb Sterical clashes 0.560585885486 Working directory is prot-na_15 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 211 393 prot-na_1000.pdb Sterical clashes 0.5368956743 Contacts, str_name: 1 182 443 prot-na_1001.pdb Sterical clashes 0.410835214447 Contacts, str_name: 2 135 353 prot-na_1002.pdb Sterical clashes 0.382436260623 Contacts, str_name: 3 160 330 prot-na_1003.pdb Sterical clashes 0.484848484848 Contacts, str_name: 4 214 454 prot-na_1004.pdb Sterical clashes 0.471365638767 Contacts, str_name: 5 196 359 prot-na_1005.pdb Sterical clashes 0.545961002786 Working directory is prot-na_20 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 93 234 prot-na_1000.pdb Sterical clashes 0.397435897436 Contacts, str_name: 1 38 159 prot-na_1001.pdb Sterical clashes 0.238993710692 Contacts, str_name: 2 68 182 prot-na_1002.pdb Sterical clashes 0.373626373626 Contacts, str_name: 3 29 133 prot-na_1003.pdb Sterical clashes 0.218045112782 Contacts, str_name: 4 27 103 prot-na_1004.pdb Sterical clashes 0.26213592233 Contacts, str_name: 5 30 119 prot-na_1005.pdb Sterical clashes 0.252100840336 Working directory is prot-na_25 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 14 97 prot-na_1000.pdb Sterical clashes 0.144329896907 Contacts, str_name: 1 28 120 prot-na_1001.pdb Sterical clashes 0.233333333333 Contacts, str_name: 2 18 110 prot-na_1002.pdb Sterical clashes 0.163636363636 Contacts, str_name: 3 32 148 prot-na_1003.pdb Sterical clashes 0.216216216216 Contacts, str_name: 4 8 68 prot-na_1004.pdb Sterical clashes 0.117647058824 Contacts, str_name: 5 11 74 prot-na_1005.pdb Sterical clashes 0.148648648649 Working directory is prot-na_30 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 6 66 prot-na_1000.pdb Sterical clashes 0.0909090909091 Contacts, str_name: 1 7 66 prot-na_1001.pdb Sterical clashes 0.106060606061 Contacts, str_name: 2 12 122 prot-na_1002.pdb Sterical clashes 0.0983606557377 Contacts, str_name: 3 19 77 prot-na_1003.pdb Sterical clashes 0.246753246753 Contacts, str_name: 4 18 86 prot-na_1004.pdb Sterical clashes 0.209302325581 Contacts, str_name: 5 13 68 prot-na_1005.pdb Sterical clashes 0.191176470588 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 390 610 prot-na_1000.pdb Sterical clashes 0.639344262295 Contacts, str_name: 1 441 727 prot-na_1001.pdb Sterical clashes 0.606602475928 Contacts, str_name: 2 491 769 prot-na_1002.pdb Sterical clashes 0.638491547464 Contacts, str_name: 3 438 713 prot-na_1003.pdb Sterical clashes 0.614305750351 Contacts, str_name: 4 449 673 prot-na_1004.pdb Sterical clashes 0.667161961367 Contacts, str_name: 5 457 705 prot-na_1005.pdb Sterical clashes 0.648226950355 There are 0.635688824627 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 5 74 prot-na_1000.pdb Sterical clashes 0.0675675675676 Contacts, str_name: 1 10 96 prot-na_1001.pdb Sterical clashes 0.104166666667 Contacts, str_name: 2 5 64 prot-na_1002.pdb Sterical clashes 0.078125 Contacts, str_name: 3 1 72 prot-na_1003.pdb Sterical clashes 0.0138888888889 Contacts, str_name: 4 0 53 prot-na_1004.pdb Sterical clashes 0.0 Contacts, str_name: 5 12 103 prot-na_1005.pdb Sterical clashes 0.116504854369 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 N THR A 5 ', 'ATOM 1121 N LEU B 6 '] ['ATOM 1 P A C 1 ', 'ATOM 406 P A D 1 '] Sat May 23 01:17:06 2026 /home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/d013c7ca-f2a8-4f9e-896a-80f204c15f16/prot-na_10 -name prot-na_*.pdb > list1.txt {'A': []} {'C': []} run_gramm1::no filtering, list1.txt -> list.txt