/home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b n_dec 21 Wed May 20 03:29:03 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 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: 0 346 564 prot-na_1000.pdb Sterical clashes 0.613475177305 Contacts, str_name: 1 356 592 prot-na_1001.pdb Sterical clashes 0.601351351351 Contacts, str_name: 2 339 596 prot-na_1002.pdb Sterical clashes 0.568791946309 Contacts, str_name: 3 377 575 prot-na_1003.pdb Sterical clashes 0.655652173913 Contacts, str_name: 4 379 603 prot-na_1004.pdb Sterical clashes 0.628524046434 Contacts, str_name: 5 340 582 prot-na_1005.pdb Sterical clashes 0.584192439863 There are 0.608664522529 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 15 76 prot-na_1000.pdb Sterical clashes 0.197368421053 Contacts, str_name: 1 8 71 prot-na_1001.pdb Sterical clashes 0.112676056338 Contacts, str_name: 2 25 124 prot-na_1002.pdb Sterical clashes 0.201612903226 Contacts, str_name: 3 8 89 prot-na_1003.pdb Sterical clashes 0.0898876404494 Contacts, str_name: 4 32 140 prot-na_1004.pdb Sterical clashes 0.228571428571 Contacts, str_name: 5 19 111 prot-na_1005.pdb Sterical clashes 0.171171171171 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 7 69 prot-na_1000.pdb Sterical clashes 0.101449275362 Contacts, str_name: 1 2 58 prot-na_1001.pdb Sterical clashes 0.0344827586207 Contacts, str_name: 2 1 54 prot-na_1002.pdb Sterical clashes 0.0185185185185 Contacts, str_name: 3 3 55 prot-na_1003.pdb Sterical clashes 0.0545454545455 Contacts, str_name: 4 4 66 prot-na_1004.pdb Sterical clashes 0.0606060606061 Contacts, str_name: 5 4 63 prot-na_1005.pdb Sterical clashes 0.0634920634921 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 SER A 69 '] ["ATOM 1 O5' DC A 1 "] Wed May 20 04:03:23 2026 /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/1eea421a-71d1-4b18-acd0-81b79ed0d23b/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt