/home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac n_dec 21 Fri May 22 04:42:03 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: 0 308 498 prot-na_1000.pdb Sterical clashes 0.618473895582 Contacts, str_name: 1 329 536 prot-na_1001.pdb Sterical clashes 0.613805970149 Contacts, str_name: 2 304 483 prot-na_1002.pdb Sterical clashes 0.629399585921 Contacts, str_name: 3 335 515 prot-na_1003.pdb Sterical clashes 0.650485436893 Contacts, str_name: 4 353 524 prot-na_1004.pdb Sterical clashes 0.673664122137 Contacts, str_name: 5 339 529 prot-na_1005.pdb Sterical clashes 0.640831758034 There are 0.637776794786 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 20 92 prot-na_1000.pdb Sterical clashes 0.217391304348 Contacts, str_name: 1 20 95 prot-na_1001.pdb Sterical clashes 0.210526315789 Contacts, str_name: 2 33 134 prot-na_1002.pdb Sterical clashes 0.246268656716 Contacts, str_name: 3 23 106 prot-na_1003.pdb Sterical clashes 0.216981132075 Contacts, str_name: 4 18 114 prot-na_1004.pdb Sterical clashes 0.157894736842 Contacts, str_name: 5 10 84 prot-na_1005.pdb Sterical clashes 0.119047619048 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 1 58 prot-na_1000.pdb Sterical clashes 0.0172413793103 Contacts, str_name: 1 3 59 prot-na_1001.pdb Sterical clashes 0.0508474576271 Contacts, str_name: 2 4 39 prot-na_1002.pdb Sterical clashes 0.102564102564 Contacts, str_name: 3 6 60 prot-na_1003.pdb Sterical clashes 0.1 Contacts, str_name: 4 5 65 prot-na_1004.pdb Sterical clashes 0.0769230769231 Contacts, str_name: 5 10 57 prot-na_1005.pdb Sterical clashes 0.175438596491 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 20 P DG 2 '] Fri May 22 05:16:23 2026 /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/8e2f895c-7717-438a-a719-842a7369a5ac/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {' ': []} run_gramm1::no filtering, list1.txt -> list.txt