CORAL-Domain fixation incompatible

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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msujata92
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CORAL-Domain fixation incompatible

#1 Post by msujata92 » 2019.01.08 18:15

I am trying to do rigid body modeling for an antibody and have 6 domains.
.con file is
L1.pdb
FabH.pdb
link 19
constantFC_A.pdb
L3.pdb
FabK.pdb
link 19
constantFC_B.pdb

The domains are extracted from the homology model (which has been done by H++ server) of the original sequence.
I am always getting the error that 'Domain 6 fixation is incompatible with the initial configuration' after grouping the domains. I am grouping (1,2), (4,5) and (3,6) domains.
I tried to move the FC domain little close to the Fabs, and also increase the number of linkers to 22 (which is wrong, because it has only 19) but getting chi2 as more than 85.xxx which is really bad.
Please guide me how to solve the issue.
Thank you in advance.

Also would like know how the coral online works?
how to give .cnd and .con file as input while submitting online?

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AL
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Location: EMBL Hamburg, Germany
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CORAL online doesn't support contact conditions

#2 Post by AL » 2019.01.25 14:28

msujata92 wrote:
2019.01.08 18:15
I am always getting the error that 'Domain 6 fixation is incompatible with the initial configuration' after grouping the domains. I am grouping (1,2), (4,5) and (3,6) domains.
This means the domains 3 and 4 cannot be reasonably connected by a linker (given the distance between 5 and 6).
There is no need to group domains 3 and 6 - if they are fixed anyway, please remove this constrain and check again.
msujata92 wrote:
2019.01.08 18:15
Also would like know how the coral online works?
how to give .cnd and .con file as input while submitting online?
CORAL online has a somewhat simplified interface compared to the command-line version. It is not possible to provide contact conditions (*.cnd) in the online version, the only way of grouping the domains in the online version is by completely fixing them (that would work only for your domains 3 and 6).

I recommend you do one CORAL online run to generate all the CORAL configuration files; then you modify the configuration files if necessary and run CORAL on your PC. Grouping of the domains is done in the "interactive" command-line interface and is described in the manual.

Please note that if you'd like to fix domains 3 and 6 please make sure they are located close to the origin (x,y,z coordinates of the center of mass is close to 0,0,0) - this will improve the reliability of the computed scattering. To move them accordingly please concatenate your two domains into one pdb file, run ALPRAXIN on it and split it back to two pdb files.

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