Dear Modeller Users,
I am a new user to Modeller 7v7 and I am trying to model a protein with over
990 residues. I started in a Windows PC and all tutorial examples were
processed without a problem. However, when I replaced the structure and the
sequence from my protein, Modeller crashed with a stack overflow error. I
got the following error message.
forrtl: severe (170): Program Exception - stack overflow
Image PC Routine Line Source
mod7v7.exe 00507271 Unknown Unknown Unknown
mod7v7.exe 004FEA3E Unknown Unknown Unknown
mod7v7.exe 004589DE Unknown Unknown Unknown
mod7v7.exe 0040653E Unknown Unknown Unknown
mod7v7.exe 0040F5BB Unknown Unknown Unknown
mod7v7.exe 006A564B Unknown Unknown Unknown
mod7v7.exe 006EDB39 Unknown Unknown Unknown
mod7v7.exe 006DC824 Unknown Unknown Unknown
kernel32.dll 7C816D4F Unknown Unknown Unknown
Then I tried with the modified version of Modeller (Updated Binary
Version), only to find the same stack overflow error. So my first question
is, is there a way to get around this and still do my analysis in a Windows
PC?
As a second attempt, I tried the same set of TOP files in a Linux
environment. Unfortunately, I couldn't get to work even the simplest TOP
scripts in Linux environment. For instance, the following script and log
shows a set that runs fine in the Windows environment but not in the Linux.
I assume that this is a result of a simple mistake. How do I fix this? Can
someone suggest a way to get this done either in Windows or in Linux?
Thank you!
Cham
TOP script:
INCLUDE
SET ALNFILE = 'TvLDH-4mdhA.ali'
SET KNOWNS = '4mdh'
SET SEQUENCE = 'TvLDH'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
CALL ROUTINE = 'model'
LOG file:
assgn___544E> Variable name not recognized: ALNFILE
Command line: SET ALNFILE = 'TvLDH-4mdhA.ali'
assgn___525E> Error in TOP variable assignment.
assgn___544E> Variable name not recognized: KNOWNS
Command line: SET KNOWNS = '4mdh'
assgn___525E> Error in TOP variable assignment.
assgn___544E> Variable name not recognized: STARTING_MODEL
Command line: SET STARTING_MODEL = 1
assgn___525E> Error in TOP variable assignment.
assgn___544E> Variable name not recognized: ENDING_MODEL
Command line: SET ENDING_MODEL = 5
assgn___525E> Error in TOP variable assignment.
compile_563E> Please correct the errors reported above and rerun MODELLER.
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 56755
55.425 0.054
Starting time : 2005/02/10
09:17:56.036
Closing time : 2005/02/10
09:17:58.468
Total CPU time [seconds] : 2.37
ALI file:
>P1;4mdh
structureX:4mdh: 1 :A: 333 :A:undefined:undefined:-1.00:-1.00
SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEI
AFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKEN
FSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITT
VQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVE
GLPINDFSREKMDLTAKELAEEKETAFEFLSSA*
>P1;TvLDH
sequence:TvLDH: : : : ::: 0.00: 0.00
SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEI
AFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKEN
FSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITT
VQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVE
GLPINDFSREKMDLTAKELAEEKETAFEFLSSA*