> A colleague in my lab. has a cacodylate molecule covalently bound to her
> structure and would like to know how she can specify the attacthment of
> this group to a cysteine on the protein for refinement in XPLOR. We have
> toplogy and parameter files for cacodylate but are unsure of the patch
> we need to use to specify the bond.
>Here's a few clues.
In your parameter file, you will need to include the bond lengths,
bond angles and any dihedrals and impropers that span the covalent
linkage between the cystein and cacodylate. It is a good idea
to use non standard atom types for the cystein so that the modified
cystein is different from the others.
Now, in your topology file, you will need to include a PATCH.
Use the presidue statement to do this. eg:
PRESidue DISU { disulfide bridge ...CYS CYS...
\DISU/ }
GROUP
MODIfy ATOM 1CB CHARge= 0.19 END
MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END
GROUP
MODIfy ATOM 2CB CHARge= 0.19 END
MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END
ADD BOND 1SG 2SG
ADD ANGLe 1CB 1SG 2SG
ADD ANGLe 1SG 2SG 2CB
ADD DIHEdral 1CA 1CB 1SG 2SG
ADD DIHEdral 1CB 1SG 2SG 2CB
ADD DIHEdral 1SG 2SG 2CB 2CA
END {DISU}
In this example the atom types of the CYS residues are changed
from SH1E to S. Yoy probably don't have to worry about modifying
the charges, but it is essential to modify the atom types of the CYS.
Finally, you will need to specify your patch after
topology, parameter and coordinates have been specified in your
xplor run, e.g:
patch
reference=1=( resid 15 and segid A) reference=2=( resid 1 and segid C)
end
Cheers,
Aaron
