/home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f n_dec 21 Sun Jul 26 21:02:02 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/64c6590c-39ff-461a-b324-72d5dc660b6f /home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f /home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f /home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f /home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f 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 Log: ['\n', '*** ERROR: for na and prot molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.5 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: 0 329 530 na-prot_1001.pdb Sterical clashes 0.620754716981 Contacts, str_name: 1 307 524 na-prot_1005.pdb Sterical clashes 0.585877862595 Contacts, str_name: 2 320 543 na-prot_1003.pdb Sterical clashes 0.589318600368 Contacts, str_name: 3 302 527 na-prot_1002.pdb Sterical clashes 0.573055028463 Contacts, str_name: 4 294 529 na-prot_1004.pdb Sterical clashes 0.555765595463 Contacts, str_name: 5 325 531 na-prot_1000.pdb Sterical clashes 0.612052730697 There are 0.589470755761 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: 0 266 500 na-prot_1001.pdb Sterical clashes 0.532 Contacts, str_name: 1 248 497 na-prot_1005.pdb Sterical clashes 0.498993963783 Contacts, str_name: 2 247 468 na-prot_1003.pdb Sterical clashes 0.527777777778 Contacts, str_name: 3 250 454 na-prot_1002.pdb Sterical clashes 0.550660792952 Contacts, str_name: 4 269 481 na-prot_1004.pdb Sterical clashes 0.559251559252 Contacts, str_name: 5 315 529 na-prot_1000.pdb Sterical clashes 0.595463137996 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: 0 207 380 na-prot_1001.pdb Sterical clashes 0.544736842105 Contacts, str_name: 1 102 289 na-prot_1005.pdb Sterical clashes 0.352941176471 Contacts, str_name: 2 95 246 na-prot_1003.pdb Sterical clashes 0.386178861789 Contacts, str_name: 3 111 289 na-prot_1002.pdb Sterical clashes 0.384083044983 Contacts, str_name: 4 139 310 na-prot_1004.pdb Sterical clashes 0.448387096774 Contacts, str_name: 5 59 221 na-prot_1000.pdb Sterical clashes 0.266968325792 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 10 91 na-prot_1001.pdb Sterical clashes 0.10989010989 Contacts, str_name: 1 21 65 na-prot_1005.pdb Sterical clashes 0.323076923077 Contacts, str_name: 2 35 101 na-prot_1003.pdb Sterical clashes 0.346534653465 Contacts, str_name: 3 53 154 na-prot_1002.pdb Sterical clashes 0.344155844156 Contacts, str_name: 4 15 82 na-prot_1004.pdb Sterical clashes 0.182926829268 Contacts, str_name: 5 19 71 na-prot_1000.pdb Sterical clashes 0.267605633803 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 23 87 na-prot_1001.pdb Sterical clashes 0.264367816092 Contacts, str_name: 1 19 85 na-prot_1005.pdb Sterical clashes 0.223529411765 Contacts, str_name: 2 5 62 na-prot_1003.pdb Sterical clashes 0.0806451612903 Contacts, str_name: 3 6 82 na-prot_1002.pdb Sterical clashes 0.0731707317073 Contacts, str_name: 4 22 111 na-prot_1004.pdb Sterical clashes 0.198198198198 Contacts, str_name: 5 5 76 na-prot_1000.pdb Sterical clashes 0.0657894736842 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 5 40 na-prot_1001.pdb Sterical clashes 0.125 Contacts, str_name: 1 6 75 na-prot_1005.pdb Sterical clashes 0.08 Contacts, str_name: 2 16 98 na-prot_1003.pdb Sterical clashes 0.163265306122 Contacts, str_name: 3 11 65 na-prot_1002.pdb Sterical clashes 0.169230769231 Contacts, str_name: 4 19 80 na-prot_1004.pdb Sterical clashes 0.2375 Contacts, str_name: 5 14 74 na-prot_1000.pdb Sterical clashes 0.189189189189 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... ['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: 0 261 509 na-prot_1001.pdb Sterical clashes 0.512770137525 Contacts, str_name: 1 284 525 na-prot_1005.pdb Sterical clashes 0.540952380952 Contacts, str_name: 2 251 504 na-prot_1003.pdb Sterical clashes 0.498015873016 Contacts, str_name: 3 271 512 na-prot_1002.pdb Sterical clashes 0.529296875 Contacts, str_name: 4 220 476 na-prot_1004.pdb Sterical clashes 0.46218487395 Contacts, str_name: 5 266 518 na-prot_1000.pdb Sterical clashes 0.513513513514 There are 0.509455608993 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 6 76 na-prot_1001.pdb Sterical clashes 0.0789473684211 Contacts, str_name: 1 14 105 na-prot_1005.pdb Sterical clashes 0.133333333333 Contacts, str_name: 2 11 71 na-prot_1003.pdb Sterical clashes 0.154929577465 Contacts, str_name: 3 3 66 na-prot_1002.pdb Sterical clashes 0.0454545454545 Contacts, str_name: 4 9 89 na-prot_1004.pdb Sterical clashes 0.101123595506 Contacts, str_name: 5 20 111 na-prot_1000.pdb Sterical clashes 0.18018018018 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' G A 1 "] ['ATOM 1 N THR A 1 '] Sun Jul 26 22:10:10 2026 /home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f/prot-na_10/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/64c6590c-39ff-461a-b324-72d5dc660b6f/prot-na_10 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt