I've got a frustrating problem when I try to run a modeller job. I know
it works as I've used it previously. I have seen the error before on
the bulletin board but can't find the cause of my problem.
I get the error:
read_al_375E> Unknown residue type,position,sequence: 1 1
I don't have any alt conformations. any help would be great. I have
attached the top and ali files.
Cheers
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Ph +64 3 4797293
Fax +64 3 4797034
MODELLER 6v2, 17 Feb 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux allroy.otago.ac.nz 2.6.5-1.358smp x86_64
Date and time of compilation : 07/16/2002 11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2004/10/29 16:08:43.499
TOP_________> 106 706 SET ALNFILE = 'UP_human_ecoli'
TOP_________> 107 707 SET KNOWNS = '1rxc_mono'
TOP_________> 108 708 SET MD_LEVEL = 'refine_3'
TOP_________> 109 709 SET SEQUENCE = '1uph'
TOP_________> 110 710 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 111 711 SET OUTPUT_DIRECTORY = './'
TOP_________> 112 712 SET PDB_EXT = '.pdb'
TOP_________> 113 713 SET ALIGNMENT_FORMAT = 'PIR'
TOP_________> 114 714 SET STARTING_MODEL = 1
TOP_________> 115 715 SET ENDING_MODEL = 5
TOP_________> 116 716 SET DEVIATION = 4.000000
TOP_________> 117 717 SET FINAL_MALIGN3D = 1
TOP_________> 118 718 SET DO_LOOPS = 1
TOP_________> 119 719 SET RADII_FACTOR = 0.915
TOP_________> 120 720 SET LOOP_STARTING_MODEL = 1
TOP_________> 121 721 SET LOOP_ENDING_MODEL = 5
TOP_________> 122 722 SET LOOP_MD_LEVEL = 'refine_2'
TOP_________> 123 723 CALL ROUTINE = 'model'
TOP_________> 124 399 CALL ROUTINE = 'getnames'
TOP_________> 125 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION;
= 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA;
TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 126 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI;
ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE;
NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE;
'
TOP_________> 127 511 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 128 512 STRING_OPERATE OPERATION = 'CONCATENATE', ;
STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI;
LE
TOP_________> 129 513 SET ROOT_NAME = SEQUENCE
TOP_________> 130 514 RETURN
TOP_________> 131 400 CALL ROUTINE = 'homcsr'
TOP_________> 132 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103
openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 6262261 6115.489 5.972
openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali
read_al_375E> Unknown residue type,position,sequence: 1 1
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 6262261 6115.489 5.972
Starting time : 2004/10/29 16:08:43.499
Closing time : 2004/10/29 16:08:44.900
Total CPU time [seconds] : 1.38
INCLUDE # remove all the #'d bits. TOP FILE FOR EXTENSIVE REFINEMENT
SET INITIAL_MALIGN3D = 1 # don't worry about this.
SET OUTPUT_CONTROL = 1 1 1 1 1 # don't worry about this either
SET ALNFILE = 'UP_human_ecoli' # alignment file, worry about this
SET KNOWNS = '1rxc_mono' # refers to xtal name in algnmnt
SET MD_LEVEL = 'refine_3' # sets simulated annealing level 1 high 3 low. 3 good to tansfer coords and fix major gliches.
SET SEQUENCE = '1uph' # name of target seq in pir file
SET ATOM_FILES_DIRECTORY = './:../atom_files' # for modeller use. It will tell you if it can't find its atoms.
SET OUTPUT_DIRECTORY = './' # is exactly that; can alter this
SET PDB_EXT = '.pdb' # leave all structures as this
SET ALIGNMENT_FORMAT = 'PIR' # leave it this way; easier
SET STARTING_MODEL = 1 # these two define the number of
SET ENDING_MODEL = 5 # models to build. Unclear why it is this way
SET DEVIATION = 4.000000 # defines how much variation is tolerated when building your model from the randomised coords. Leave as is.
SET FINAL_MALIGN3D = 1 # don't worry about this
SET DO_LOOPS = 1 # for explicit loop building
SET RADII_FACTOR = 0.915 # the x factor for good structure. Always include this.
SET LOOP_STARTING_MODEL = 1 #back to explicit loop modeling
SET LOOP_ENDING_MODEL = 5 # i built 10 per model, 50 loops in total. Too much. 1 model 10 loops
SET LOOP_MD_LEVEL = 'refine_2' # md level used; same as above
CALL ROUTINE = 'model' # is the modeller key word for modelling building