/home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1 n_dec 21 Sun May 24 15:50:03 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for na and prot molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1 /home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1 /home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1 /home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1 /home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1 n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.2 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... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 173 337 na-prot_1001.pdb Sterical clashes 0.513353115727 Contacts, str_name: 1 204 383 na-prot_1005.pdb Sterical clashes 0.532637075718 Contacts, str_name: 2 215 372 na-prot_1003.pdb Sterical clashes 0.577956989247 Contacts, str_name: 3 181 336 na-prot_1002.pdb Sterical clashes 0.53869047619 Contacts, str_name: 4 192 351 na-prot_1004.pdb Sterical clashes 0.547008547009 Contacts, str_name: 5 164 324 na-prot_1000.pdb Sterical clashes 0.506172839506 There are 0.535969840566 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... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 116 236 na-prot_1001.pdb Sterical clashes 0.491525423729 Contacts, str_name: 1 133 282 na-prot_1005.pdb Sterical clashes 0.471631205674 Contacts, str_name: 2 144 290 na-prot_1003.pdb Sterical clashes 0.496551724138 Contacts, str_name: 3 101 246 na-prot_1002.pdb Sterical clashes 0.410569105691 Contacts, str_name: 4 110 284 na-prot_1004.pdb Sterical clashes 0.387323943662 Contacts, str_name: 5 110 298 na-prot_1000.pdb Sterical clashes 0.369127516779 Working directory is prot-na_15 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 11 98 na-prot_1001.pdb Sterical clashes 0.112244897959 Contacts, str_name: 1 20 86 na-prot_1005.pdb Sterical clashes 0.232558139535 Contacts, str_name: 2 37 130 na-prot_1003.pdb Sterical clashes 0.284615384615 Contacts, str_name: 3 25 93 na-prot_1002.pdb Sterical clashes 0.268817204301 Contacts, str_name: 4 19 93 na-prot_1004.pdb Sterical clashes 0.204301075269 Contacts, str_name: 5 32 138 na-prot_1000.pdb Sterical clashes 0.231884057971 Working directory is prot-na_20 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 24 88 na-prot_1001.pdb Sterical clashes 0.272727272727 Contacts, str_name: 1 11 56 na-prot_1005.pdb Sterical clashes 0.196428571429 Contacts, str_name: 2 7 62 na-prot_1003.pdb Sterical clashes 0.112903225806 Contacts, str_name: 3 6 47 na-prot_1002.pdb Sterical clashes 0.127659574468 Contacts, str_name: 4 13 64 na-prot_1004.pdb Sterical clashes 0.203125 Contacts, str_name: 5 6 31 na-prot_1000.pdb Sterical clashes 0.193548387097 Working directory is prot-na_25 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 9 43 na-prot_1001.pdb Sterical clashes 0.209302325581 Contacts, str_name: 1 5 62 na-prot_1005.pdb Sterical clashes 0.0806451612903 Contacts, str_name: 2 4 44 na-prot_1003.pdb Sterical clashes 0.0909090909091 Contacts, str_name: 3 8 45 na-prot_1002.pdb Sterical clashes 0.177777777778 Contacts, str_name: 4 6 41 na-prot_1004.pdb Sterical clashes 0.146341463415 Contacts, str_name: 5 2 42 na-prot_1000.pdb Sterical clashes 0.047619047619 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 OP3 C A 1 '] ['ATOM 1 N THR A 1 '] Sun May 24 16:24:04 2026 /home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1/prot-na_25/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/0c17a33b-57b0-4db6-9093-e9acf9d964c1/prot-na_25 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt