[modeller_usage] rdactio_534E> Command not recognized: INPUT :
To:
Subject: [modeller_usage] rdactio_534E> Command not recognized: INPUT :
From: Joseph Toth <>
Date: Mon, 27 Oct 2003 17:27:32 -0500
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