/home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634 n_dec 21 Wed Feb 25 10:48:03 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/47024cd7-f6de-4299-af1a-8da840fea634 /home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634 /home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634 /home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634 /home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634 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 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: 0 180 242 na-prot_1001.pdb Sterical clashes 0.743801652893 Contacts, str_name: 1 182 242 na-prot_1005.pdb Sterical clashes 0.752066115702 Contacts, str_name: 2 183 242 na-prot_1003.pdb Sterical clashes 0.756198347107 Contacts, str_name: 3 187 242 na-prot_1002.pdb Sterical clashes 0.772727272727 Contacts, str_name: 4 193 242 na-prot_1004.pdb Sterical clashes 0.797520661157 Contacts, str_name: 5 176 242 na-prot_1000.pdb Sterical clashes 0.727272727273 There are 0.75826446281 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: 0 142 222 na-prot_1001.pdb Sterical clashes 0.63963963964 Contacts, str_name: 1 184 242 na-prot_1005.pdb Sterical clashes 0.760330578512 Contacts, str_name: 2 170 242 na-prot_1003.pdb Sterical clashes 0.702479338843 Contacts, str_name: 3 181 236 na-prot_1002.pdb Sterical clashes 0.766949152542 Contacts, str_name: 4 170 242 na-prot_1004.pdb Sterical clashes 0.702479338843 Contacts, str_name: 5 172 241 na-prot_1000.pdb Sterical clashes 0.713692946058 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 35 134 na-prot_1001.pdb Sterical clashes 0.261194029851 Contacts, str_name: 1 41 126 na-prot_1005.pdb Sterical clashes 0.325396825397 Contacts, str_name: 2 39 113 na-prot_1003.pdb Sterical clashes 0.345132743363 Contacts, str_name: 3 14 89 na-prot_1002.pdb Sterical clashes 0.157303370787 Contacts, str_name: 4 13 82 na-prot_1004.pdb Sterical clashes 0.158536585366 Contacts, str_name: 5 36 135 na-prot_1000.pdb Sterical clashes 0.266666666667 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 14 90 na-prot_1001.pdb Sterical clashes 0.155555555556 Contacts, str_name: 1 18 71 na-prot_1005.pdb Sterical clashes 0.253521126761 Contacts, str_name: 2 14 85 na-prot_1003.pdb Sterical clashes 0.164705882353 Contacts, str_name: 3 3 58 na-prot_1002.pdb Sterical clashes 0.051724137931 Contacts, str_name: 4 13 105 na-prot_1004.pdb Sterical clashes 0.12380952381 Contacts, str_name: 5 16 78 na-prot_1000.pdb Sterical clashes 0.205128205128 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 59 na-prot_1001.pdb Sterical clashes 0.101694915254 Contacts, str_name: 1 13 66 na-prot_1005.pdb Sterical clashes 0.19696969697 Contacts, str_name: 2 8 49 na-prot_1003.pdb Sterical clashes 0.163265306122 Contacts, str_name: 3 8 67 na-prot_1002.pdb Sterical clashes 0.119402985075 Contacts, str_name: 4 10 77 na-prot_1004.pdb Sterical clashes 0.12987012987 Contacts, str_name: 5 7 55 na-prot_1000.pdb Sterical clashes 0.127272727273 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 OP3 DA A 1 '] ['ATOM 4134 N MET B 1 '] Wed Feb 25 11:24:18 2026 /home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634/prot-na_25/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/47024cd7-f6de-4299-af1a-8da840fea634/prot-na_25 -name na-prot_*.pdb > list1.txt {'A': []} {'B': []} run_gramm1::no filtering, list1.txt -> list.txt