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*