CORAL: Domain Fixation Order problem

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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mawhite
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CORAL: Domain Fixation Order problem

#1 Post by mawhite » 2016.05.27 19:59

Hello,

I am having a problem similar to the previous post "CORAL domain configutation issues". However, the problem is slightly different. The error

"Domain *: fixation is not compatible with initial configuration"

depends on the choice and order of the domains. The fixed domain, a heptameric pore forming domain, is the C-terminal of three domains. This ordering produces the "fixation is not compatible" error. when the order of the domains is reversed, but not the liner spacing, linker length, or domain positions, everything works fine.

Thank you for the answer to the previous CORAL post, I always manually position the domains at a reasonable position to each other, but never realized that this was critical for CORAL to function.

luker
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Re: CORAL: Domain Fixation Order problem

#2 Post by luker » 2016.09.14 22:22

Hi -

I am having the identical problem as reported below. It seems that CORAL does not allow the first domain to be free and the second domain to be fixed: I am able to do a run in which the first domain is fixed and the second is free, but not the other way around.

I am a novice at this, so sorry if I have missed something obvious. But I don't see a simple workaround for the Nter-Domain1-linker-Domain2 case I am working on becausesecond domain is in three separate pieces because of disordered loops I have not been able to build in the crystal structure. So, I want to have those three pieces fixed in their original position, thereby preventing the domain from flying apart (this works fine in EOM with the same PDB files, by the way).

Any help about how to get around this problem would be much appreciated.

Thanks,

Luke

Alex
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Re: CORAL: Domain Fixation Order problem

#3 Post by Alex » 2016.09.15 11:54

I had similar errors but typically when i fix my domains too far and linker is too short to connect them. Luke, can you post your t.con file content?
How big are you disordered loops?
Alex

luker
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Re: CORAL: Domain Fixation Order problem

#4 Post by luker » 2016.09.16 18:47

Alex -

Thanks for your reply. It prompted me to re-examine my domain separation. In doing so realized that I had moved the wrong termini close to each other. CORAL runs fine for me now keeping the pieces of my second domain fixed. Apologies for the false alarm.

Luke

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