/home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412 n_dec 21 Wed Apr 29 03:58:03 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/306afc2b-547c-441b-9165-7fde0380a412 /home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412 /home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412 /home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412 /home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412 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 Log: ['\n', '*** ERROR: for na and prot molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.4 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: 0 334 718 na-prot_1001.pdb Sterical clashes 0.465181058496 Contacts, str_name: 1 342 711 na-prot_1005.pdb Sterical clashes 0.481012658228 Contacts, str_name: 2 310 709 na-prot_1003.pdb Sterical clashes 0.437235543018 Contacts, str_name: 3 277 679 na-prot_1002.pdb Sterical clashes 0.40795287187 Contacts, str_name: 4 295 708 na-prot_1004.pdb Sterical clashes 0.416666666667 Contacts, str_name: 5 323 692 na-prot_1000.pdb Sterical clashes 0.46676300578 There are 0.445801967343 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: 0 277 610 na-prot_1001.pdb Sterical clashes 0.454098360656 Contacts, str_name: 1 237 618 na-prot_1005.pdb Sterical clashes 0.383495145631 Contacts, str_name: 2 215 592 na-prot_1003.pdb Sterical clashes 0.363175675676 Contacts, str_name: 3 273 638 na-prot_1002.pdb Sterical clashes 0.42789968652 Contacts, str_name: 4 254 590 na-prot_1004.pdb Sterical clashes 0.430508474576 Contacts, str_name: 5 269 644 na-prot_1000.pdb Sterical clashes 0.417701863354 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 72 265 na-prot_1001.pdb Sterical clashes 0.271698113208 Contacts, str_name: 1 42 201 na-prot_1005.pdb Sterical clashes 0.208955223881 Contacts, str_name: 2 104 350 na-prot_1003.pdb Sterical clashes 0.297142857143 Contacts, str_name: 3 64 234 na-prot_1002.pdb Sterical clashes 0.273504273504 Contacts, str_name: 4 61 239 na-prot_1004.pdb Sterical clashes 0.255230125523 Contacts, str_name: 5 79 282 na-prot_1000.pdb Sterical clashes 0.280141843972 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 50 152 na-prot_1001.pdb Sterical clashes 0.328947368421 Contacts, str_name: 1 30 113 na-prot_1005.pdb Sterical clashes 0.265486725664 Contacts, str_name: 2 12 64 na-prot_1003.pdb Sterical clashes 0.1875 Contacts, str_name: 3 6 68 na-prot_1002.pdb Sterical clashes 0.0882352941176 Contacts, str_name: 4 25 109 na-prot_1004.pdb Sterical clashes 0.229357798165 Contacts, str_name: 5 19 106 na-prot_1000.pdb Sterical clashes 0.179245283019 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 6 38 na-prot_1001.pdb Sterical clashes 0.157894736842 Contacts, str_name: 1 4 68 na-prot_1005.pdb Sterical clashes 0.0588235294118 Contacts, str_name: 2 8 70 na-prot_1003.pdb Sterical clashes 0.114285714286 Contacts, str_name: 3 14 83 na-prot_1002.pdb Sterical clashes 0.168674698795 Contacts, str_name: 4 11 62 na-prot_1004.pdb Sterical clashes 0.177419354839 Contacts, str_name: 5 23 84 na-prot_1000.pdb Sterical clashes 0.27380952381 Working directory is prot-na_30 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 3 48 na-prot_1001.pdb Sterical clashes 0.0625 Contacts, str_name: 1 14 76 na-prot_1005.pdb Sterical clashes 0.184210526316 Contacts, str_name: 2 12 43 na-prot_1003.pdb Sterical clashes 0.279069767442 Contacts, str_name: 3 9 70 na-prot_1002.pdb Sterical clashes 0.128571428571 Contacts, str_name: 4 8 70 na-prot_1004.pdb Sterical clashes 0.114285714286 Contacts, str_name: 5 7 58 na-prot_1000.pdb Sterical clashes 0.120689655172 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 1 "] ['ATOM 1 N SER A 69 '] Wed Apr 29 04:33:03 2026 /home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412/prot-na_30/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/306afc2b-547c-441b-9165-7fde0380a412/prot-na_30 -name na-prot_*.pdb > list1.txt {' ': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt