GAJOE terminates prematurely

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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Alexandra
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Posts: 21
Joined: 2008.11.26 06:32

GAJOE terminates prematurely

#1 Post by Alexandra » 2010.09.07 04:15

Hi:

I have run Ranch and generated pdbs (all in the same directory as the *dat file), now I am trying to run GAJOE on Linux using the default setting, but here is the error I get:

CYCLE: 49
Initial genes created
Starting Genetic Algorithm
CYCLE: 50
Initial genes created
Starting Genetic Algorithm
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
mv: cannot stat `04557.pdb': No such file or directory
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
mv: cannot stat `05688.pdb': No such file or directory
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
mv: cannot stat `06780.pdb': No such file or directory
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
mv: cannot stat `07831.pdb': No such file or directory
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
list in: end of file
apparent state: internal I/O
lately reading direct formatted internal IO
No such file or directory
Experimental file Zero_alexpool_B2and3and5

It looks like to program cannot files the files? Is there a specific naming/directory structure one needs?

Thanks,
Alex

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Hayds
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Posts: 101
Joined: 2008.05.21 19:01
Location: EMBL, Hamburg

#2 Post by Hayds » 2010.09.10 17:30

Hi Alex,

so the generations are complete up until 50? Then the error message appears?

Which version of EOM (ranch/gajoe) are you using and on what OS?

I have not seen this behavior so I think I will need as much info as you can give.

Cheers,

Haydyn

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Hayds
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Posts: 101
Joined: 2008.05.21 19:01
Location: EMBL, Hamburg

#3 Post by Hayds » 2010.09.10 17:32

Oh, also. If you have the distribution of EOM that includes example files, try from a fresh directory and run through this and see if the error still occurs.

h

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