/home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e n_dec 21 Fri Oct 23 17:05:03 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/f6f9702c-8193-4f6d-850f-79335bec5b3e /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e 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 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: 0 571 782 prot-na_1000.pdb Sterical clashes 0.730179028133 Contacts, str_name: 1 609 801 prot-na_1001.pdb Sterical clashes 0.760299625468 Contacts, str_name: 2 542 801 prot-na_1002.pdb Sterical clashes 0.676654182272 Contacts, str_name: 3 629 786 prot-na_1003.pdb Sterical clashes 0.800254452926 Contacts, str_name: 4 612 797 prot-na_1004.pdb Sterical clashes 0.767879548306 Contacts, str_name: 5 567 789 prot-na_1005.pdb Sterical clashes 0.718631178707 There are 0.742316335969 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: 0 540 799 prot-na_1000.pdb Sterical clashes 0.675844806008 Contacts, str_name: 1 586 797 prot-na_1001.pdb Sterical clashes 0.735257214555 Contacts, str_name: 2 557 782 prot-na_1002.pdb Sterical clashes 0.712276214834 Contacts, str_name: 3 585 793 prot-na_1003.pdb Sterical clashes 0.737704918033 Contacts, str_name: 4 535 776 prot-na_1004.pdb Sterical clashes 0.689432989691 Contacts, str_name: 5 514 765 prot-na_1005.pdb Sterical clashes 0.671895424837 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 81 270 prot-na_1000.pdb Sterical clashes 0.3 Contacts, str_name: 1 236 499 prot-na_1001.pdb Sterical clashes 0.472945891784 Contacts, str_name: 2 153 347 prot-na_1002.pdb Sterical clashes 0.440922190202 Contacts, str_name: 3 85 249 prot-na_1003.pdb Sterical clashes 0.341365461847 Contacts, str_name: 4 183 468 prot-na_1004.pdb Sterical clashes 0.391025641026 Contacts, str_name: 5 58 208 prot-na_1005.pdb Sterical clashes 0.278846153846 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 7 104 prot-na_1000.pdb Sterical clashes 0.0673076923077 Contacts, str_name: 1 37 116 prot-na_1001.pdb Sterical clashes 0.318965517241 Contacts, str_name: 2 59 171 prot-na_1002.pdb Sterical clashes 0.345029239766 Contacts, str_name: 3 13 157 prot-na_1003.pdb Sterical clashes 0.0828025477707 Contacts, str_name: 4 26 166 prot-na_1004.pdb Sterical clashes 0.156626506024 Contacts, str_name: 5 21 108 prot-na_1005.pdb Sterical clashes 0.194444444444 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 5 83 prot-na_1000.pdb Sterical clashes 0.0602409638554 Contacts, str_name: 1 10 91 prot-na_1001.pdb Sterical clashes 0.10989010989 Contacts, str_name: 2 18 116 prot-na_1002.pdb Sterical clashes 0.155172413793 Contacts, str_name: 3 9 86 prot-na_1003.pdb Sterical clashes 0.104651162791 Contacts, str_name: 4 21 136 prot-na_1004.pdb Sterical clashes 0.154411764706 Contacts, str_name: 5 41 173 prot-na_1005.pdb Sterical clashes 0.236994219653 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 ALA A 22 '] ["ATOM 1 O5' G A 1 "] Fri Oct 23 17:42:01 2026 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_25/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_25 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt