/home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab n_dec 21 Fri Mar 13 11:22:04 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/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab /home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab /home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab /home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab /home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab 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 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: 0 118 210 prot-na_1000.pdb Sterical clashes 0.561904761905 Contacts, str_name: 1 150 217 prot-na_1001.pdb Sterical clashes 0.691244239631 Contacts, str_name: 2 147 218 prot-na_1002.pdb Sterical clashes 0.674311926606 Contacts, str_name: 3 126 221 prot-na_1003.pdb Sterical clashes 0.570135746606 Contacts, str_name: 4 140 202 prot-na_1004.pdb Sterical clashes 0.693069306931 Contacts, str_name: 5 120 214 prot-na_1005.pdb Sterical clashes 0.560747663551 There are 0.625235607538 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 74 156 prot-na_1000.pdb Sterical clashes 0.474358974359 Contacts, str_name: 1 74 160 prot-na_1001.pdb Sterical clashes 0.4625 Contacts, str_name: 2 50 172 prot-na_1002.pdb Sterical clashes 0.290697674419 Contacts, str_name: 3 59 137 prot-na_1003.pdb Sterical clashes 0.430656934307 Contacts, str_name: 4 63 154 prot-na_1004.pdb Sterical clashes 0.409090909091 Contacts, str_name: 5 78 193 prot-na_1005.pdb Sterical clashes 0.40414507772 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 9 84 prot-na_1000.pdb Sterical clashes 0.107142857143 Contacts, str_name: 1 14 88 prot-na_1001.pdb Sterical clashes 0.159090909091 Contacts, str_name: 2 7 65 prot-na_1002.pdb Sterical clashes 0.107692307692 Contacts, str_name: 3 14 100 prot-na_1003.pdb Sterical clashes 0.14 Contacts, str_name: 4 8 92 prot-na_1004.pdb Sterical clashes 0.0869565217391 Contacts, str_name: 5 15 106 prot-na_1005.pdb Sterical clashes 0.141509433962 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 MET 1 '] ['ATOM 1 P DG S 1 '] Fri Mar 13 11:56:35 2026 /home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/7b5911c9-e2b9-4b75-b0b6-1fcb80bb1eab/prot-na_15 -name prot-na_*.pdb > list1.txt {' ': []} {'S': []} run_gramm1::no filtering, list1.txt -> list.txt