/home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901 n_dec 21 Thu Mar 12 06:59:05 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/47e36bed-9275-4d42-84c3-9519ce9c9901 /home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901 /home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901 /home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901 /home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901 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: 0 338 561 prot-na_1000.pdb Sterical clashes 0.602495543672 Contacts, str_name: 1 348 601 prot-na_1001.pdb Sterical clashes 0.579034941764 Contacts, str_name: 2 308 570 prot-na_1002.pdb Sterical clashes 0.540350877193 Contacts, str_name: 3 326 579 prot-na_1003.pdb Sterical clashes 0.563039723661 Contacts, str_name: 4 356 603 prot-na_1004.pdb Sterical clashes 0.590381426202 Contacts, str_name: 5 361 668 prot-na_1005.pdb Sterical clashes 0.540419161677 There are 0.569286945695 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: 0 288 603 prot-na_1000.pdb Sterical clashes 0.477611940299 Contacts, str_name: 1 265 516 prot-na_1001.pdb Sterical clashes 0.513565891473 Contacts, str_name: 2 280 525 prot-na_1002.pdb Sterical clashes 0.533333333333 Contacts, str_name: 3 250 486 prot-na_1003.pdb Sterical clashes 0.514403292181 Contacts, str_name: 4 237 430 prot-na_1004.pdb Sterical clashes 0.551162790698 Contacts, str_name: 5 284 599 prot-na_1005.pdb Sterical clashes 0.474123539232 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 37 146 prot-na_1000.pdb Sterical clashes 0.253424657534 Contacts, str_name: 1 37 169 prot-na_1001.pdb Sterical clashes 0.218934911243 Contacts, str_name: 2 78 197 prot-na_1002.pdb Sterical clashes 0.395939086294 Contacts, str_name: 3 57 175 prot-na_1003.pdb Sterical clashes 0.325714285714 Contacts, str_name: 4 70 211 prot-na_1004.pdb Sterical clashes 0.331753554502 Contacts, str_name: 5 96 220 prot-na_1005.pdb Sterical clashes 0.436363636364 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 16 98 prot-na_1000.pdb Sterical clashes 0.163265306122 Contacts, str_name: 1 11 85 prot-na_1001.pdb Sterical clashes 0.129411764706 Contacts, str_name: 2 26 179 prot-na_1002.pdb Sterical clashes 0.145251396648 Contacts, str_name: 3 44 129 prot-na_1003.pdb Sterical clashes 0.341085271318 Contacts, str_name: 4 15 75 prot-na_1004.pdb Sterical clashes 0.2 Contacts, str_name: 5 16 76 prot-na_1005.pdb Sterical clashes 0.210526315789 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 13 90 prot-na_1000.pdb Sterical clashes 0.144444444444 Contacts, str_name: 1 7 83 prot-na_1001.pdb Sterical clashes 0.0843373493976 Contacts, str_name: 2 12 71 prot-na_1002.pdb Sterical clashes 0.169014084507 Contacts, str_name: 3 16 93 prot-na_1003.pdb Sterical clashes 0.172043010753 Contacts, str_name: 4 3 63 prot-na_1004.pdb Sterical clashes 0.047619047619 Contacts, str_name: 5 29 99 prot-na_1005.pdb Sterical clashes 0.292929292929 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 8 100 prot-na_1000.pdb Sterical clashes 0.08 Contacts, str_name: 1 6 77 prot-na_1001.pdb Sterical clashes 0.0779220779221 Contacts, str_name: 2 10 64 prot-na_1002.pdb Sterical clashes 0.15625 Contacts, str_name: 3 5 70 prot-na_1003.pdb Sterical clashes 0.0714285714286 Contacts, str_name: 4 16 76 prot-na_1004.pdb Sterical clashes 0.210526315789 Contacts, str_name: 5 9 75 prot-na_1005.pdb Sterical clashes 0.12 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 CYS A 166 '] ["ATOM 1 O5' G A 1 "] Thu Mar 12 07:37:20 2026 /home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901/prot-na_30/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/47e36bed-9275-4d42-84c3-9519ce9c9901/prot-na_30 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt