/home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974 n_dec 21 Thu Apr 30 00:44:04 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/3d535c15-f95f-433b-a81b-4c51c7dd5974 /home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974 /home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974 /home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974 /home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974 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: 0 426 815 na-prot_1001.pdb Sterical clashes 0.522699386503 Contacts, str_name: 1 442 845 na-prot_1005.pdb Sterical clashes 0.523076923077 Contacts, str_name: 2 433 829 na-prot_1003.pdb Sterical clashes 0.522316043426 Contacts, str_name: 3 419 820 na-prot_1002.pdb Sterical clashes 0.510975609756 Contacts, str_name: 4 419 820 na-prot_1004.pdb Sterical clashes 0.510975609756 Contacts, str_name: 5 425 852 na-prot_1000.pdb Sterical clashes 0.49882629108 There are 0.514811643933 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: 0 239 587 na-prot_1001.pdb Sterical clashes 0.407155025554 Contacts, str_name: 1 228 564 na-prot_1005.pdb Sterical clashes 0.404255319149 Contacts, str_name: 2 280 662 na-prot_1003.pdb Sterical clashes 0.422960725076 Contacts, str_name: 3 269 653 na-prot_1002.pdb Sterical clashes 0.411944869832 Contacts, str_name: 4 335 723 na-prot_1004.pdb Sterical clashes 0.463347164592 Contacts, str_name: 5 321 737 na-prot_1000.pdb Sterical clashes 0.435549525102 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 5 75 na-prot_1001.pdb Sterical clashes 0.0666666666667 Contacts, str_name: 1 30 112 na-prot_1005.pdb Sterical clashes 0.267857142857 Contacts, str_name: 2 20 97 na-prot_1003.pdb Sterical clashes 0.20618556701 Contacts, str_name: 3 11 98 na-prot_1002.pdb Sterical clashes 0.112244897959 Contacts, str_name: 4 11 88 na-prot_1004.pdb Sterical clashes 0.125 Contacts, str_name: 5 13 76 na-prot_1000.pdb Sterical clashes 0.171052631579 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 23 108 na-prot_1001.pdb Sterical clashes 0.212962962963 Contacts, str_name: 1 6 46 na-prot_1005.pdb Sterical clashes 0.130434782609 Contacts, str_name: 2 12 76 na-prot_1003.pdb Sterical clashes 0.157894736842 Contacts, str_name: 3 3 64 na-prot_1002.pdb Sterical clashes 0.046875 Contacts, str_name: 4 5 63 na-prot_1004.pdb Sterical clashes 0.0793650793651 Contacts, str_name: 5 7 63 na-prot_1000.pdb Sterical clashes 0.111111111111 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' DC A 1 "] ['ATOM 1 N SER A 69 '] Thu Apr 30 01:19:29 2026 /home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974/prot-na_20/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/3d535c15-f95f-433b-a81b-4c51c7dd5974/prot-na_20 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt