Very new here any help would be great! When I get this figured out I
am going to do some documentation for dummies on this.
When I run 'mod sequence_search' I get an error "fullfn__230E> File not
found: very-short-for-test.cod" What is the .cod file? Here is a
copy of my script.
# Example for: SEQUENCE_SEARCH
# This will search the MODELLER database of representative protein
chains
# for chains similar to the specified sequence.
SET OUTPUT_CONTROL = 1 1 1 1 1
SET SEARCH_RANDOMIZATIONS = 20 # should use 100 in real life;
SET GAP_PENALTIES_1D = -800 -400
SET SEARCH_CHAINS_LIST = 'very-short-for-test.cod'
SEQUENCE_SEARCH FILE = 'P450.ali', ALIGN_CODES = '1nbt'
MALIGN
WRITE_ALIGNMENT FILE = 'toxin-search.pap', ALIGNMENT_FORMAT = 'PAP'
So I made a file called "very-short-for-test.cod"
I then get an error in this log:
Date and time of compilation : 07/19/2002 11:38:41
Job starting time (YY/MM/DD HH:MM:SS): 2002/10/15 14:49:24.094
Dynamically allocated memory at amaxseq [B,kB,MB]: 2200483
2148.909 2.099
TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 20
TOP_________> 3 3 SET GAP_PENALTIES_1D = -800 -400
TOP_________> 4 4 SET SEARCH_CHAINS_LIST =
'very-short-for-test.cod'
TOP_________> 5 5 SEQUENCE_SEARCH FILE = 'P450.ali', ALIGN_CODES
= '1nbt'
openf5__224_> Open 11 OLD SEQUENTIAL very-short-for-test.cod
amaxchn_215E> Dynamic memory allocation failed.
Routine, variable, status: iseqdb 3
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2200483
2148.909 2.099
Starting time : 2002/10/15
14:49:24.094
Closing time : 2002/10/15
14:49:28.614
Total CPU time [seconds] : 4.36
thank you for any help!
