/home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b n_dec 21 Thu Apr 30 10:18:04 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 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: 0 397 818 na-prot_1001.pdb Sterical clashes 0.48533007335 Contacts, str_name: 1 418 830 na-prot_1005.pdb Sterical clashes 0.503614457831 Contacts, str_name: 2 368 788 na-prot_1003.pdb Sterical clashes 0.467005076142 Contacts, str_name: 3 400 805 na-prot_1002.pdb Sterical clashes 0.496894409938 Contacts, str_name: 4 404 792 na-prot_1004.pdb Sterical clashes 0.510101010101 Contacts, str_name: 5 401 800 na-prot_1000.pdb Sterical clashes 0.50125 There are 0.49403250456 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 72 206 na-prot_1001.pdb Sterical clashes 0.349514563107 Contacts, str_name: 1 61 133 na-prot_1005.pdb Sterical clashes 0.458646616541 Contacts, str_name: 2 91 260 na-prot_1003.pdb Sterical clashes 0.35 Contacts, str_name: 3 37 170 na-prot_1002.pdb Sterical clashes 0.217647058824 Contacts, str_name: 4 33 182 na-prot_1004.pdb Sterical clashes 0.181318681319 Contacts, str_name: 5 13 130 na-prot_1000.pdb Sterical clashes 0.1 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 4 55 na-prot_1001.pdb Sterical clashes 0.0727272727273 Contacts, str_name: 1 9 86 na-prot_1005.pdb Sterical clashes 0.104651162791 Contacts, str_name: 2 5 73 na-prot_1003.pdb Sterical clashes 0.0684931506849 Contacts, str_name: 3 12 65 na-prot_1002.pdb Sterical clashes 0.184615384615 Contacts, str_name: 4 1 60 na-prot_1004.pdb Sterical clashes 0.0166666666667 Contacts, str_name: 5 8 54 na-prot_1000.pdb Sterical clashes 0.148148148148 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 10:52:52 2026 /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b/prot-na_15/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/2fb38514-2b4e-489f-93ca-21c7102b143b/prot-na_15 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt