[phenixbb] covalently linked ligand

[Pavel Afonine]

Hi,

in addition to Nigel's reply, here is what I typically do:

you can define a bond between any pair of atoms (any number of such 
bonds), just like this:

refinement.geometry_restraints.edits {
   bond {
     atom_selection_1 = chain A and resseq 1 and name N
     atom_selection_2 = chain A and resseq 2 and name O
     distance_ideal = 1.3
     sigma = 0.02
   }
   bond {
     atom_selection_1 = chain A and resseq 2 and name O
     atom_selection_2 = chain X and resseq 3 and name C
     distance_ideal = 1.4
     sigma = 0.04
   }
}

That is, save the lines above in a  file and give this  file to 
phenix.refine either in the command line or in the GUI.

Let us know (through phenixbb) if you have any questions or problems 
related to this.

All the best,
Pavel


On 6/8/12 9:40 AM, Charles Stewart Jr., PhD wrote:
> Hello all,
>
> I saw a couple of posts on this from a year ago but didn't find a
> conclusive answer to how to tell phenix to insert a covalent bond between
> a cysteine residue  and a bound inhibitor. I have the inhibitor (a small
> molecule) modeled in but haven't figured out how to insert the covalent
> bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a
> cif file. The distance between the sulfur on the cysteine and the first
> carbon atom in the inhibitor is 1.8A.
>
> Do I need to run eLBOW using the protein-inhibitor pdb to generate an
> appropriate cif file?
>
> I see in phenix.refine under the PDB interpretation tab their is a box for
> "add link to CIF"....is this where I need to tell phenix to insert the
> covalent bond?
>
> I guess I could just draw the inhibitor-cysteine complex as a modified
> amino acid and try inserting it that way.....
>
> charles