[Chimera-users] minmize small molecule

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 6 12:07:12 PDT 2009

The "Minimize Structure" tool in Chimera uses MMTK.  In general, it  
works on (polyatomic) nonstandard residues because Antechamber is can  
generate parameters for those, but unfortunately there is a hard  
limitation on the types of monatomic atoms that are handled.

 From the Minimize Structure documentation:
"Only the ions in ff99 are handled: Na+, K+, Rb+, Cs+, Mg2+, Ca2+,  
Zn2+, and Cl–"

You could change the Cu to one of those, say Mg, by editing your  
structure input file or by using Build Structure (Modify Atom  
section).  If you are concerned about the effect on the nearby atoms,  
you could make sure to freeze that part of the structure so that it is  
not allowed to move during minimization.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 6, 2009, at 10:35 AM, Venkataraman Kabaleeswaran wrote:

> Hi
> I wanted to optimize the geometry of small molecule by minimization  
> for docking.
> I have not seen any option in chimera but even I did tried with the  
> small molecule I have as nonstandard aminoacid, but it give me error  
> mmtrk could not Cu atom type.
> Is it any small script or through chimera I could able to optimize  
> the small molecule?
> thanks
> Kabaleeswaran Venkataraman

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