[gmx-users] Metalloproteins-creation of topology files

bruno.rizzuti at email.it bruno.rizzuti at email.it
Tue Feb 8 11:22:56 CET 2005

  chandran karunakaran wrote: 
Dear GMX user, 

  I am interested in plastocyanine, ie metalloprotein molecular dynamics
using GMX toplology and force field parameters. 

Cannistraro and coworkers have been investigating this protein using both
the Gromos and Charmm force field. The Cu ion is difficult to model because
the coordination is different with respect to model compounds. You should
derive your own parameters if you are interested in the detailed behavior of
the active site. Otherwise, using constraints to attach the Cu ion to the
polipeptide chain -though being a crude approximation- could be enough in
some cases. 

  I assumed the Cu(II) and coordinating 
aminoacid residues as one moiety and gave 
atomic numbering and name. But I got error. I would be happy if someone
advise me how to do it. 

You can try to define a moiety formed by the Cys coordinating residue + the
Cu ion, and then to define interaction of the Cu with the other ligands. It
worked for me to simulate azurin with the Encad force field. In any case,
you have to define parameters (force constants, partial charges etc.) of
your own. 

Greetings, Bruno.  
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