Hi,
I am trying to do the modeller tutorial on a linux machine, with version mod7v7.
After running seq_search for the TvDLH model the seqsearch.dat is empty, and I get the .log file as shown below.
Would you know why I can't get any answer from my search?
Thanks, Paula.
Kind, OS, HostName, Kernel, Processor: 4, Linux japiim.cbi.cnptia.embrapa.br 2.4.20-42.9.legacysmp i 686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/04/11 16:50:46.106
Dynamically allocated memory at amaxseq [B,kB,MB]: 69639 68.007 0.066 TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 100
TOP_________> 3 3 SET MAXRES = 300
TOP_________> 4 4 SET FILE = 'TvLDH.seq'
TOP_________> 5 5 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON
Dynamically allocated memory at amaxseq [B,kB,MB]: 614337 599.938 0.586
Dynamically allocated memory at amaxbnd [B,kB,MB]: 32806393 32037.492 31.287 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.seq
Searching a list of chains for similarity with a given sequence:
Target sequence : TvLDH.seq List of test chains : ${MODINSTALL7v7}/modlib//CHAINS_3.0_40_XN.cod Number of test chains : 0 Residue-residue metric: ${MODINSTALL7v7}/modlib//as1.sim.mat Gap penalties U, V : -900.00 -50.00 Randomizations : 100 +/- range for sig2&3 : 10 SIGNIF_CUTOFF : 4.00 5.00 Top chains are listed : 20 (see the corresponding $MODINSTALL/modlib/seqfilt_*.grp file for more related PDB codes)
RELATED_SEQUENCES
# CODE_1 CODE_2 LEN1 LEN2 NID %ID %ID SCORE SIGNI SIGNI2 SIGNI3 ----------------------------------------------------------------------------- ---
openf5__224_> Open 14 UNKNOWN SEQUENTIAL seqsearch.dat
Dynamically allocated memory at finish [B,kB,MB]: 32806393 32037.492 31.287 Starting time : 2005/04/11 16:50:46.106 Closing time : 2005/04/11 16:50:46.882 Total CPU time [seconds] : 0.58
Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária