/home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4 n_dec 21 Mon May 25 15:48:03 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4 /home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4 /home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4 /home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4 /home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4 n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.1 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 267 491 prot-na_1000.pdb Sterical clashes 0.543788187373 Contacts, str_name: 1 215 426 prot-na_1001.pdb Sterical clashes 0.504694835681 Contacts, str_name: 2 282 524 prot-na_1002.pdb Sterical clashes 0.538167938931 Contacts, str_name: 3 222 440 prot-na_1003.pdb Sterical clashes 0.504545454545 Contacts, str_name: 4 264 465 prot-na_1004.pdb Sterical clashes 0.567741935484 Contacts, str_name: 5 274 548 prot-na_1005.pdb Sterical clashes 0.5 There are 0.526489725336 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 289 523 prot-na_1000.pdb Sterical clashes 0.55258126195 Contacts, str_name: 1 235 459 prot-na_1001.pdb Sterical clashes 0.511982570806 Contacts, str_name: 2 213 448 prot-na_1002.pdb Sterical clashes 0.475446428571 Contacts, str_name: 3 223 477 prot-na_1003.pdb Sterical clashes 0.46750524109 Contacts, str_name: 4 234 481 prot-na_1004.pdb Sterical clashes 0.486486486486 Contacts, str_name: 5 205 439 prot-na_1005.pdb Sterical clashes 0.466970387244 Working directory is prot-na_15 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 177 412 prot-na_1000.pdb Sterical clashes 0.429611650485 Contacts, str_name: 1 197 365 prot-na_1001.pdb Sterical clashes 0.539726027397 Contacts, str_name: 2 153 395 prot-na_1002.pdb Sterical clashes 0.387341772152 Contacts, str_name: 3 226 480 prot-na_1003.pdb Sterical clashes 0.470833333333 Contacts, str_name: 4 160 384 prot-na_1004.pdb Sterical clashes 0.416666666667 Contacts, str_name: 5 223 507 prot-na_1005.pdb Sterical clashes 0.439842209073 Working directory is prot-na_20 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 94 244 prot-na_1000.pdb Sterical clashes 0.385245901639 Contacts, str_name: 1 137 323 prot-na_1001.pdb Sterical clashes 0.424148606811 Contacts, str_name: 2 107 315 prot-na_1002.pdb Sterical clashes 0.339682539683 Contacts, str_name: 3 73 221 prot-na_1003.pdb Sterical clashes 0.330316742081 Contacts, str_name: 4 98 231 prot-na_1004.pdb Sterical clashes 0.424242424242 Contacts, str_name: 5 95 283 prot-na_1005.pdb Sterical clashes 0.335689045936 Working directory is prot-na_25 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 94 234 prot-na_1000.pdb Sterical clashes 0.401709401709 Contacts, str_name: 1 46 179 prot-na_1001.pdb Sterical clashes 0.256983240223 Contacts, str_name: 2 60 195 prot-na_1002.pdb Sterical clashes 0.307692307692 Contacts, str_name: 3 56 221 prot-na_1003.pdb Sterical clashes 0.253393665158 Contacts, str_name: 4 68 202 prot-na_1004.pdb Sterical clashes 0.336633663366 Contacts, str_name: 5 56 174 prot-na_1005.pdb Sterical clashes 0.32183908046 Working directory is prot-na_30 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 19 124 prot-na_1000.pdb Sterical clashes 0.153225806452 Contacts, str_name: 1 67 201 prot-na_1001.pdb Sterical clashes 0.333333333333 Contacts, str_name: 2 20 86 prot-na_1002.pdb Sterical clashes 0.232558139535 Contacts, str_name: 3 32 126 prot-na_1003.pdb Sterical clashes 0.253968253968 Contacts, str_name: 4 32 161 prot-na_1004.pdb Sterical clashes 0.198757763975 Contacts, str_name: 5 43 137 prot-na_1005.pdb Sterical clashes 0.313868613139 It is no appropriate decoys in the high resolution docking. Low resolution docking is starting! gramm scan now gramm scan now gramm scan now gramm scan now gramm scan now gramm scan now gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 155 402 prot-na_1000.pdb Sterical clashes 0.385572139303 Contacts, str_name: 1 175 416 prot-na_1001.pdb Sterical clashes 0.420673076923 Contacts, str_name: 2 159 402 prot-na_1002.pdb Sterical clashes 0.39552238806 Contacts, str_name: 3 118 375 prot-na_1003.pdb Sterical clashes 0.314666666667 Contacts, str_name: 4 170 424 prot-na_1004.pdb Sterical clashes 0.400943396226 Contacts, str_name: 5 165 423 prot-na_1005.pdb Sterical clashes 0.390070921986 There are 0.384574764861 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 5 67 prot-na_1000.pdb Sterical clashes 0.0746268656716 Contacts, str_name: 1 6 52 prot-na_1001.pdb Sterical clashes 0.115384615385 Contacts, str_name: 2 10 92 prot-na_1002.pdb Sterical clashes 0.108695652174 Contacts, str_name: 3 5 42 prot-na_1003.pdb Sterical clashes 0.119047619048 Contacts, str_name: 4 11 80 prot-na_1004.pdb Sterical clashes 0.1375 Contacts, str_name: 5 5 60 prot-na_1005.pdb Sterical clashes 0.0833333333333 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 N ASP A 1 ', 'ATOM 320 N ASP B 1 ', 'ATOM 639 N ASP C 1 ', 'ATOM 958 N ASP D 1 '] ["ATOM 1 O5' DC 1 "] Mon May 25 17:07:07 2026 /home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/3d2bb143-3bc2-4ebe-a9dc-5e4881dfbdf4/prot-na_10 -name prot-na_*.pdb > list1.txt {'A': []} {' ': []} run_gramm1::no filtering, list1.txt -> list.txt