/home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464 n_dec 21 Mon Apr 27 11:09:04 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/67904ee6-0e01-4791-8992-7bca1c6c3464 /home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464 /home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464 /home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464 /home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464 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: 0 286 435 prot-na_1000.pdb Sterical clashes 0.657471264368 Contacts, str_name: 1 251 380 prot-na_1001.pdb Sterical clashes 0.660526315789 Contacts, str_name: 2 265 405 prot-na_1002.pdb Sterical clashes 0.654320987654 Contacts, str_name: 3 280 413 prot-na_1003.pdb Sterical clashes 0.677966101695 Contacts, str_name: 4 232 382 prot-na_1004.pdb Sterical clashes 0.607329842932 Contacts, str_name: 5 267 413 prot-na_1005.pdb Sterical clashes 0.646489104116 There are 0.650683936092 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 62 170 prot-na_1000.pdb Sterical clashes 0.364705882353 Contacts, str_name: 1 132 292 prot-na_1001.pdb Sterical clashes 0.452054794521 Contacts, str_name: 2 99 243 prot-na_1002.pdb Sterical clashes 0.407407407407 Contacts, str_name: 3 117 259 prot-na_1003.pdb Sterical clashes 0.451737451737 Contacts, str_name: 4 171 315 prot-na_1004.pdb Sterical clashes 0.542857142857 Contacts, str_name: 5 112 264 prot-na_1005.pdb Sterical clashes 0.424242424242 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 16 86 prot-na_1000.pdb Sterical clashes 0.186046511628 Contacts, str_name: 1 5 61 prot-na_1001.pdb Sterical clashes 0.0819672131148 Contacts, str_name: 2 14 96 prot-na_1002.pdb Sterical clashes 0.145833333333 Contacts, str_name: 3 12 88 prot-na_1003.pdb Sterical clashes 0.136363636364 Contacts, str_name: 4 30 108 prot-na_1004.pdb Sterical clashes 0.277777777778 Contacts, str_name: 5 7 107 prot-na_1005.pdb Sterical clashes 0.0654205607477 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 GLY A 1 '] ['ATOM 17 P DC L 2 '] Mon Apr 27 11:43:20 2026 /home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/67904ee6-0e01-4791-8992-7bca1c6c3464/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {'L': []} run_gramm1::no filtering, list1.txt -> list.txt