how to apply patches (PRESidue) in CNS_SOLVE

Wolfram Tempel tempel at linus.bmb.uga.edu
Thu May 25 09:48:15 EST 2000


Hi,
For a carbohydrate-based ligand I would like to set-up
topology/parameters for refinement in CNS_SOLVE.  The appropriate sugar
residues are present in the provided $CNS_TOPPAR/carbohydrate.* as are
most of the patches I require (alpha links etc.).  But how do I actually
apply these patches? I only found the example for the di-sulfide patch
(in the news group):

*******************************************************************************************

topology @TOPPAR:tophcsdx.pro end
! [lots of other stuff omited for clarity]
! Patch in disulfides
patch DISU
    reference=1=( resid 9 and segid D )
    reference=2=( resid 86 and segid D )
end
patch DISU
    reference=1=( resid 9 and segid E )
    reference=2=( resid 86 and segid E )
end
*******************************************************************************************

Am I supposed to actually edit $CNS_TOPPAR/carbohydrate.top?
And how do I transfer the example's syntax to carbohydrates, e.g. for a
linkage patch?
Also, are there any suggestions for how to patch for a methyl glycoside?

Thank you in advance.

Wolfram



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