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
Joe,
Separate the elements of the KNOWNS array (SET KNOWNS = ...) with individual quotes for each element like '1cvj' '1g2e' etc.
Eswar.
-----Original Message----- From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Joseph Toth Sent: Monday, October 27, 2003 2:28 PM To: modeller_usage@salilab.org 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 _______________________________________________ modeller_usage mailing list modeller_usage@salilab.org http://salilab.org/mailman/listinfo/modeller_usage
participants (2)
-
Eswar Narayanan -
Joseph Toth