[phenixbb] Ligand restraints editing with REEL

Joseph Brock joeylives2ride at hotmail.com
Sat Sep 18 01:09:23 PDT 2010

Hi all,

I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. 

I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc).

I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes.

Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them.

Thanks so much in advance.



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