[Chimera-users] minmize small molecule

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 6 14:51:57 PDT 2009

It looks like the Cu is part of the small molecule.  Sorry, in my  
first reply I thought it was just a separate monatomic ion (not  
covalently bonded to anything) that happened to be near the small  
molecule, such as in the binding site of a protein.

Covalent organometallic compounds cannot be minimized in Chimera.   
Chimera uses Antechamber/GAFF to assign parameters to nonstandard  
residues such as small molecules, and this process is only meant to  
handle organic molecules made of C, N, O, H, S, P, F, Cl, Br and I.

To minimize this type of compound, you would need to use some other  
program, sorry.

On Jul 6, 2009, at 12:48 PM, Venkataraman Kabaleeswaran wrote:

> changed the atom type, but got the following error message?
> Running ANTECHAMBER command: /net/earth/disk3/vk/pgm/chimera/bin/ 
> antechamber/exe/antechamber -i /tmp/tmpXaquvp/ante.in.mol2 -fi mol2 - 
> o /tmp/tmpXaquvp/ante.out.mol2 -fo mol2 -c gas -nc -1 -df 0 -j 5 -s 2
> (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ 
> ac -j part
> (LIG)
> (LIG) For atom[10]:Mg, the best APS is not zero, exit
> (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ 
> atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> (LIG)
> (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ 
> atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "/net/ 
> earth/disk3/vk/pgm/chimera/bin/antechamber"/dat/antechamber/ 
> (LIG)
> (LIG)
> (LIG) No Gasteiger parameter for atom[9]:Mg  :DU, exit(0)
> Failure running ANTECHAMBER for residue LIG
> Check reply log for details
> Kabaleeswaran Venkataraman
> --------------------------------------------------------------
> Arise, Awake and stop not until goal is Reached
>                                       - Swami Vivekananda
> --------------------------------------------------------------
> --- On Mon, 7/6/09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] minmize small molecule
> To: "Venkataraman Kabaleeswaran" <vkabs at yahoo.com>
> Cc: chimera-users at cgl.ucsf.edu
> Date: Monday, July 6, 2009, 8:07 PM
> Hello,
> 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–"
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html 
> >
> 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
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 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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