I get a "command not recognized" error, see log below when trying to use the 'special_patches' routine, to tell modeller to make 2 S-S bonds in a loop I am modelling,
I can't see any error in my top file or alignment,
I used the code directly from the manual FAQ number 6, define additional disulphides not in template, with appropriate changes, see top file below.
any ideas what I am doing wrong?
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'loop1.ali' # alignment filename SET KNOWNS = '4DPV' # codes of the templates SET SEQUENCE = 'lop1' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' STOP
# Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): SUBROUTINE ROUTINE = 'special_patches' # A disulfide between residues 226 and 234 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '226:A' '234:A' # A disulfide between residues 228 and 232 in chain A: PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '228:A' '232:A' RETURN END_SUBROUTINE
Kind, OS, HostName, Kernel, Processor: 4, Linux modeling.bio.jyu.fi 2.6.8-1.521 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/12 15:04:54.106
rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2004/10/12 15:04:54.106 Closing time : 2004/10/12 15:04:55.092 Total CPU time [seconds] : 0.94
>P1;4DPV-CPVVP-withDNAZ structure:4DPV:22 :Z:593 :Z:::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVEITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAQIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSE----PPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGT---------SGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNEYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY* >P1;COAT_PAVC2_VP2 sequence:lop1:22 :A:593 : :A::: GSGNGSGGGGGGGSGGVGISTGTFNNQTEFKFLENGWVYITANSSRLVHLNMPESENYRR VVVNNMDKTAVNGNMALDDIHAEIVTPWSLVDANAWGVWFNPGDWQLIVNTMSELHLVSF EQEIFNVVLKTVSESATQPPTKVYNNDLTASLMVALDSNNTMPFTPAAMRSETLGFYPWK PTIPTPWRYYFQWDRTLIPSHTGTCDCRGDCFCSGTPTNIYHGTDPDDVQFYTIENSVPVHLLRTGDEF ATGTFFFDCKPCRLTHTWQTNRALGLPPFLNSLPQSEGATNFGDIGVQQDKRRGVTQMGN TNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAFG RQHGKKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKTG INYTNIFNTYGPLTALNNVPPVYPNGQIWDKEFDTDLKPRLHVNAPFVCQNNCPGQLFVK VAPNLTNQYDPDASANMSRIVTYSDFWWKGKLVFKAKLRASHTWNPIQQMSINVDNQFNY VPSNIGGMKIVYEKSQLAPRKLY*
Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile)
http://www.chalkie.org.uk firstname.lastname@example.org email@example.com
On Tue, Oct 12, 2004 at 03:18:57PM +0300, Dr. Daniel James White PhD wrote: > I get a "command not recognized" error, see log below when trying to > use the 'special_patches' routine, > to tell modeller to make 2 S-S bonds in a loop I am modelling, > > I can't see any error in my top file or alignment,
We solved this problem off the list; the problem is that one of the lines in the TOP file contained some blank space followed by a # comment. Ordinarily, this is not a problem, but in this instance there were some tab characters within that blank space, and this confused Modeller. The workaround for the current version is not to use tabs in TOP files (Modeller converts them internally into space characters anyway). This bug will be fixed in future Modeller releases.
Ben Webb, Modeller Caretaker