/home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0 n_dec 21 Fri Oct 23 12:16:02 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/d0c280cb-2ab6-427b-a7a4-b709e96386b0 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0 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: 0 760 1258 prot-na_1000.pdb Sterical clashes 0.60413354531 Contacts, str_name: 1 747 1226 prot-na_1001.pdb Sterical clashes 0.609298531811 Contacts, str_name: 2 740 1195 prot-na_1002.pdb Sterical clashes 0.619246861925 Contacts, str_name: 3 791 1257 prot-na_1003.pdb Sterical clashes 0.629276054097 Contacts, str_name: 4 754 1231 prot-na_1004.pdb Sterical clashes 0.612510154346 Contacts, str_name: 5 740 1245 prot-na_1005.pdb Sterical clashes 0.59437751004 There are 0.611473776255 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: 0 734 1295 prot-na_1000.pdb Sterical clashes 0.566795366795 Contacts, str_name: 1 593 1091 prot-na_1001.pdb Sterical clashes 0.543538038497 Contacts, str_name: 2 492 991 prot-na_1002.pdb Sterical clashes 0.496468213925 Contacts, str_name: 3 639 1097 prot-na_1003.pdb Sterical clashes 0.582497721057 Contacts, str_name: 4 526 1022 prot-na_1004.pdb Sterical clashes 0.514677103718 Contacts, str_name: 5 541 998 prot-na_1005.pdb Sterical clashes 0.542084168337 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: 0 160 335 prot-na_1000.pdb Sterical clashes 0.477611940299 Contacts, str_name: 1 90 265 prot-na_1001.pdb Sterical clashes 0.339622641509 Contacts, str_name: 2 110 374 prot-na_1002.pdb Sterical clashes 0.294117647059 Contacts, str_name: 3 144 379 prot-na_1003.pdb Sterical clashes 0.379947229551 Contacts, str_name: 4 138 359 prot-na_1004.pdb Sterical clashes 0.384401114206 Contacts, str_name: 5 189 377 prot-na_1005.pdb Sterical clashes 0.501326259947 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 29 195 prot-na_1000.pdb Sterical clashes 0.148717948718 Contacts, str_name: 1 53 184 prot-na_1001.pdb Sterical clashes 0.288043478261 Contacts, str_name: 2 24 132 prot-na_1002.pdb Sterical clashes 0.181818181818 Contacts, str_name: 3 27 116 prot-na_1003.pdb Sterical clashes 0.23275862069 Contacts, str_name: 4 28 137 prot-na_1004.pdb Sterical clashes 0.204379562044 Contacts, str_name: 5 23 96 prot-na_1005.pdb Sterical clashes 0.239583333333 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 24 99 prot-na_1000.pdb Sterical clashes 0.242424242424 Contacts, str_name: 1 24 84 prot-na_1001.pdb Sterical clashes 0.285714285714 Contacts, str_name: 2 16 102 prot-na_1002.pdb Sterical clashes 0.156862745098 Contacts, str_name: 3 16 105 prot-na_1003.pdb Sterical clashes 0.152380952381 Contacts, str_name: 4 16 62 prot-na_1004.pdb Sterical clashes 0.258064516129 Contacts, str_name: 5 7 86 prot-na_1005.pdb Sterical clashes 0.0813953488372 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 10 92 prot-na_1000.pdb Sterical clashes 0.108695652174 Contacts, str_name: 1 19 139 prot-na_1001.pdb Sterical clashes 0.136690647482 Contacts, str_name: 2 5 66 prot-na_1002.pdb Sterical clashes 0.0757575757576 Contacts, str_name: 3 8 75 prot-na_1003.pdb Sterical clashes 0.106666666667 Contacts, str_name: 4 6 64 prot-na_1004.pdb Sterical clashes 0.09375 Contacts, str_name: 5 14 89 prot-na_1005.pdb Sterical clashes 0.157303370787 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 MET B 1 ', 'ATOM 1070 N GLU C 10 '] ['ATOM 2555 P A R 1 '] Fri Oct 23 13:06:08 2026 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/prot-na_30/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/prot-na_30 -name prot-na_*.pdb > list1.txt {'B': []} {'R': []} run_gramm1::no filtering, list1.txt -> list.txt