[modeller_usage] error on 'special_patches' routine for PATCH S-S bonds

["Dr. Daniel James White PhD" <>]

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