[phenixbb] ligand refinement - elbow

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Sat Mar 1 07:42:55 PST 2008


I would highly recommend using SMILES strings as input in elbow. This eliminates the ambiguities inherent in assigning bond orders using PDB files. Othwerwise you could build the ligand in a molecular modeling package, minimize it using either a force field or quantum mechanics package, leave the hydrogens on so the program can figure out the bond orders if the connect records are absent, and export this as PDB for input into elbow. This approach is a bit redundant, but works too. 



> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Christine Gee
> Sent: Friday, February 29, 2008 7:28 PM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] ligand refinement - elbow
> Hi
> Its taken me a while to get around to it, but I just ran elbow to  
> create a cif file etc for my inhibitor, but the bond lengths are  
> quite different from what I got from the PRODRUG server, and 
> it seems  
> that the pdb file I got out of elbow has a few problems (COOT 
> doesn't  
> join up the aromatic ring for example because the carbons are 
> now too  
> far away on one part of the ring). I was wondering how the bond  
> lengths are selected?  It seems it is giving the aromatic carbons a  
> bond length of 1.5, when my previous file (and phenylalanine for  
> example have 1.3).  Also, I still am not 100% sure how to add the  
> CONNECT information to make the ligand able to covalently 
> bind to the  
> protein.
> Regards
> Christine
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