RE: [modeller_usage] rdactio_534E> Command not recognized: INPUT :

["Eswar Narayanan" <>]

Joe,

Separate the elements of the KNOWNS array (SET KNOWNS = ...) with individual
quotes for each element like '1cvj' '1g2e' etc.

Eswar.


-----Original Message-----
From: 
[">mailto:] On Behalf Of Joseph Toth
Sent: Monday, October 27, 2003 2:28 PM
To: 
Subject: [modeller_usage] rdactio_534E> Command not recognized: INPUT :

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
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