[buster-discuss] Dimethylysine restraints

[Axelrod, Herbert L.]

Hi,
 I am trying to refine a protein in which the lysine residues have been reductively methylated. In the input coordinate file, I have re-named the LYS residues to MLY. To setup restraints for MLY residues, I have implemented PDB2TNT to output a restraints dictionary for MLY using the idealized coordinates found in Ligand Expo. When I try to input this dictionary using the -l option of BUSTER, I get the following error message in ab_pdb2tnt


############################# 1. initial checks ##############################
 
 
 ####################### 2. creating TNT sequence file ########################
 
 
 ########################### 3. processing residues ###########################
 
 
 ###################### 4. processing missing restraints ######################
 
 
 ####################### 5. remove duplicate restraints #######################
 
 
 ERROR : [pdb2tnt-0023] something wrong when excluding
         "GEOMETRY [ ]*MLY [ ]*BOND[A-Z]*.* [ ]*N [ ]*CA"
         restraint from ./01-BUSTER/Cycle-1/my.geom


Obviously there is something amiss in my refinement strategy, and was wondering if anyone could suggest the proper strategy to setup restraints and implement BUSTER refinement for proteins containing methylated lysine residues.

Many Thanks,

Herb Axelrod
Staff Scientist
Stanford Synchrotron Radiation Lightsource