Hi Modellers,
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?
cheers
Dan
top file:
# 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
log file:
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
ali file:
>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 dan@chalkie.org.uk white@cc.jyu.fi