/home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430 n_dec 21 Sun Jul 26 12:18:02 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/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430 /home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430 /home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430 /home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430 /home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430 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 Log: ['\n', '*** ERROR: for na and prot molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.3 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: 0 307 529 na-prot_1001.pdb Sterical clashes 0.58034026465 Contacts, str_name: 1 315 544 na-prot_1005.pdb Sterical clashes 0.579044117647 Contacts, str_name: 2 289 504 na-prot_1003.pdb Sterical clashes 0.573412698413 Contacts, str_name: 3 309 525 na-prot_1002.pdb Sterical clashes 0.588571428571 Contacts, str_name: 4 294 512 na-prot_1004.pdb Sterical clashes 0.57421875 Contacts, str_name: 5 271 525 na-prot_1000.pdb Sterical clashes 0.51619047619 There are 0.568629622579 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: 0 249 478 na-prot_1001.pdb Sterical clashes 0.520920502092 Contacts, str_name: 1 247 490 na-prot_1005.pdb Sterical clashes 0.504081632653 Contacts, str_name: 2 226 455 na-prot_1003.pdb Sterical clashes 0.496703296703 Contacts, str_name: 3 205 392 na-prot_1002.pdb Sterical clashes 0.522959183673 Contacts, str_name: 4 248 502 na-prot_1004.pdb Sterical clashes 0.494023904382 Contacts, str_name: 5 162 383 na-prot_1000.pdb Sterical clashes 0.422976501305 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 27 126 na-prot_1001.pdb Sterical clashes 0.214285714286 Contacts, str_name: 1 41 132 na-prot_1005.pdb Sterical clashes 0.310606060606 Contacts, str_name: 2 32 130 na-prot_1003.pdb Sterical clashes 0.246153846154 Contacts, str_name: 3 52 183 na-prot_1002.pdb Sterical clashes 0.284153005464 Contacts, str_name: 4 40 127 na-prot_1004.pdb Sterical clashes 0.314960629921 Contacts, str_name: 5 22 124 na-prot_1000.pdb Sterical clashes 0.177419354839 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 9 56 na-prot_1001.pdb Sterical clashes 0.160714285714 Contacts, str_name: 1 16 79 na-prot_1005.pdb Sterical clashes 0.20253164557 Contacts, str_name: 2 12 74 na-prot_1003.pdb Sterical clashes 0.162162162162 Contacts, str_name: 3 12 85 na-prot_1002.pdb Sterical clashes 0.141176470588 Contacts, str_name: 4 11 66 na-prot_1004.pdb Sterical clashes 0.166666666667 Contacts, str_name: 5 18 82 na-prot_1000.pdb Sterical clashes 0.219512195122 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 8 48 na-prot_1001.pdb Sterical clashes 0.166666666667 Contacts, str_name: 1 8 63 na-prot_1005.pdb Sterical clashes 0.126984126984 Contacts, str_name: 2 2 37 na-prot_1003.pdb Sterical clashes 0.0540540540541 Contacts, str_name: 3 4 45 na-prot_1002.pdb Sterical clashes 0.0888888888889 Contacts, str_name: 4 8 57 na-prot_1004.pdb Sterical clashes 0.140350877193 Contacts, str_name: 5 8 69 na-prot_1000.pdb Sterical clashes 0.115942028986 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 O5' U A 1 "] ['ATOM 1 N THR A 1 '] Sun Jul 26 12:52:32 2026 /home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430/prot-na_25/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/4b2b6a8c-ebaa-4d5c-912c-35f2ee6f3430/prot-na_25 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt