/home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62 n_dec 21 Fri Jul 24 19:37:02 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/7b0a82ff-9a6b-468f-ac08-72c9319fcf62 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62 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 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: 0 358 497 prot-na_1000.pdb Sterical clashes 0.72032193159 Contacts, str_name: 1 340 483 prot-na_1001.pdb Sterical clashes 0.703933747412 Contacts, str_name: 2 359 506 prot-na_1002.pdb Sterical clashes 0.709486166008 Contacts, str_name: 3 374 500 prot-na_1003.pdb Sterical clashes 0.748 Contacts, str_name: 4 369 500 prot-na_1004.pdb Sterical clashes 0.738 Contacts, str_name: 5 365 505 prot-na_1005.pdb Sterical clashes 0.722772277228 There are 0.723752353706 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: 0 311 495 prot-na_1000.pdb Sterical clashes 0.628282828283 Contacts, str_name: 1 282 487 prot-na_1001.pdb Sterical clashes 0.579055441478 Contacts, str_name: 2 291 474 prot-na_1002.pdb Sterical clashes 0.613924050633 Contacts, str_name: 3 312 487 prot-na_1003.pdb Sterical clashes 0.640657084189 Contacts, str_name: 4 325 469 prot-na_1004.pdb Sterical clashes 0.692963752665 Contacts, str_name: 5 346 501 prot-na_1005.pdb Sterical clashes 0.690618762475 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: 0 211 352 prot-na_1000.pdb Sterical clashes 0.599431818182 Contacts, str_name: 1 202 375 prot-na_1001.pdb Sterical clashes 0.538666666667 Contacts, str_name: 2 145 279 prot-na_1002.pdb Sterical clashes 0.519713261649 Contacts, str_name: 3 198 391 prot-na_1003.pdb Sterical clashes 0.506393861893 Contacts, str_name: 4 220 430 prot-na_1004.pdb Sterical clashes 0.511627906977 Contacts, str_name: 5 214 425 prot-na_1005.pdb Sterical clashes 0.503529411765 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 78 252 prot-na_1000.pdb Sterical clashes 0.309523809524 Contacts, str_name: 1 26 122 prot-na_1001.pdb Sterical clashes 0.213114754098 Contacts, str_name: 2 94 245 prot-na_1002.pdb Sterical clashes 0.383673469388 Contacts, str_name: 3 132 363 prot-na_1003.pdb Sterical clashes 0.363636363636 Contacts, str_name: 4 101 244 prot-na_1004.pdb Sterical clashes 0.41393442623 Contacts, str_name: 5 72 239 prot-na_1005.pdb Sterical clashes 0.301255230126 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 10 110 prot-na_1000.pdb Sterical clashes 0.0909090909091 Contacts, str_name: 1 30 194 prot-na_1001.pdb Sterical clashes 0.154639175258 Contacts, str_name: 2 27 101 prot-na_1002.pdb Sterical clashes 0.267326732673 Contacts, str_name: 3 19 92 prot-na_1003.pdb Sterical clashes 0.20652173913 Contacts, str_name: 4 11 95 prot-na_1004.pdb Sterical clashes 0.115789473684 Contacts, str_name: 5 24 106 prot-na_1005.pdb Sterical clashes 0.22641509434 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 11 101 prot-na_1000.pdb Sterical clashes 0.108910891089 Contacts, str_name: 1 19 95 prot-na_1001.pdb Sterical clashes 0.2 Contacts, str_name: 2 24 124 prot-na_1002.pdb Sterical clashes 0.193548387097 Contacts, str_name: 3 21 89 prot-na_1003.pdb Sterical clashes 0.23595505618 Contacts, str_name: 4 29 95 prot-na_1004.pdb Sterical clashes 0.305263157895 Contacts, str_name: 5 17 102 prot-na_1005.pdb Sterical clashes 0.166666666667 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: 0 283 477 prot-na_1000.pdb Sterical clashes 0.593291404612 Contacts, str_name: 1 300 493 prot-na_1001.pdb Sterical clashes 0.608519269777 Contacts, str_name: 2 338 506 prot-na_1002.pdb Sterical clashes 0.667984189723 Contacts, str_name: 3 313 497 prot-na_1003.pdb Sterical clashes 0.629778672032 Contacts, str_name: 4 310 497 prot-na_1004.pdb Sterical clashes 0.623742454728 Contacts, str_name: 5 322 501 prot-na_1005.pdb Sterical clashes 0.642714570858 There are 0.627671760289 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 8 97 prot-na_1000.pdb Sterical clashes 0.0824742268041 Contacts, str_name: 1 11 87 prot-na_1001.pdb Sterical clashes 0.126436781609 Contacts, str_name: 2 12 99 prot-na_1002.pdb Sterical clashes 0.121212121212 Contacts, str_name: 3 1 58 prot-na_1003.pdb Sterical clashes 0.0172413793103 Contacts, str_name: 4 6 68 prot-na_1004.pdb Sterical clashes 0.0882352941176 Contacts, str_name: 5 12 97 prot-na_1005.pdb Sterical clashes 0.123711340206 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 GLU A 13 ', 'ATOM 777 N GLU B 13 ', 'ATOM 1552 N VAL C 14 ', 'ATOM 2304 N GLU D 13 ', 'ATOM 3070 N GLU E 13 ', 'ATOM 3845 N GLU F 13 ', 'ATOM 4616 N GLU G 13 ', 'ATOM 5382 N VAL H 14 '] ['ATOM 1 CM2 OMG A 1 '] Fri Jul 24 20:46:44 2026 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_10 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt