rdactio_534E> Command not recognized: INPUT : - modeller_usage

27 Oct 2003


      Hi,
I have been trying to run the model script and it keeps crashing with the message:
rdactio_534E> Command not recognized:  INPUT  :
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
Someone else used a similar model script successfully on the same machine but I
can't figure out what is wrong with my input files.  I would appreciate any 
suggestions.  Is this a TOP or a fortran formatting error?  How do I narrow
down the problem?
MODEL.top
# 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  = 'Pab1.seg.ali'      # alignment filename
SET KNOWNS   = '1CVJ 1G2E 1FXL 1FNX 1HL6 1P1T'  # codes of the templates
SET SEQUENCE = 'Pab1'               # code of the target
SET ATOM_FILES_DIRECTORY = './'     # 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'              # do homology modelling
Pab1.seg.ali
>P1;Pab1
sequence:Pab1:FIRST:@:LAST:@:polyadenylate-binding protein 1:Saccharomyces
cerevisiae:-1.00:-1.00
MADITDKTAEQLENLNIQDDQKQAATGSESQSVENSSASLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAIT
KTSLGYAYVNFNDHEAGRKAIEQLNYTPIKGRLCRIMWSQRDPSLRKKGSGNIFIKNLHPDIDNKALYDTFSVFG
DILSSKIATDENGKSKGFGFVHFEEEGAAKEAIDALNGMLLNGQEIYVAPHLSRKERDSQLEETKAHYTNLYVKN
INSETTDEQFQELFAKFGPIVSASLEKDADGKLKGFGFVNYEKHEDAVKAVEALNDSELNGEKLYVGRAQKKNER
MHVLKKQYEAYRLEKMAKYQGVNLFVKNLDDSVDDEKLEEEFAPYGTITSAKVMRTENGKSKGFGFVCFSTPEEA
TKAITEKNQQIVAGKPLYVAIAQRKDVRRSQLAQQIQARNQMRYQQATAAAAAAAAGMPGQFMPPMFYGVMPPRG
VPFNGPNPQQMNPMGGMPKNGMPPQFRNGPVYGVPPQGGFPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEE
AAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQEQQTEQA*
>P1;1CVJ
StructureX:1CVJ:FIRST:A:LAST:A:POLYDENYLATE BINDING PROTEIN 1:HOMO SAPIENS:
2.60: 0.23
-----------------------------------ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR
SLGYAYVNFQQPADAERALDTMNFDVIKGKPV--RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG
NILSCKV--------------------------------------------------------------------
---------------------------------------------------------------------------
----------------------------------------------------VCDENGSKGYGFVHFETQEAAER
AIEKMNGMLL-----------------------------------------------------------------
---------------------------------------------------------------------------
-------------------------------NDRKVFVGRFKSRKER-----*
...this file continues with more entries like the second
ICVJ.atm
HEADER    GENE REGULATION/RNA                     23-AUG-99   1CVJ
TITLE     X-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN
TITLE    2 COMPLEX WITH POLYADENYLATE RNA
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: POLYDENYLATE BINDING PROTEIN 1;
COMPND   3 CHAIN: A, B, C, D, E, F, G, H;
COMPND   4 FRAGMENT: RESIDUES 1-190;
...this file continues with the standard pdb format
--joe