[Chimera-users] Using mol2 files

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 3 15:30:12 PDT 2007

Hi Pasquale,
The "Minimize Structure" tool and "minimize" command will  
automatically take care of this issue for many structures.  The  
charge addition step (same as using the "Add Charge" tool) uses  
Antechamber to both calculate the partial atomic charges and assign  
types to atoms in nonstandard residues.

In fact, PDB files don't have atom types either.  But if there are  
only standard residues (standard, unmodified amino acids, nucleic  
acids, and water), the atom types and charges are simply looked up in  
the Amber parm files.  Again, this is automatically done by Chimera.

For more information on atom type and parameter assignment, see

Nonstandard residues get "gaff" types intended for use with Amber, as  
mentioned in that page (there is also a literature reference).  After  
they are assigned, you can see what the types are by custom-labeling  
those atoms with the gaffType attribute, for example for a residue  
named GLC with the following commands:

labelopt info gaffType
label :glc

So, minimizing in Chimera may already work for your structure.  Not  
everything can be handled, however - the MMTK/Amber99 parameter set  
includes many but not all metal ions, and Antechamber is not meant to  
handle inorganic molecules or metal complexes.  In such cases you may  
need to use a different program.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 3, 2007, at 12:11 PM, Pasquale Iacono wrote:

> Hi I imported a .mol2 file from Gaussian to Chimera because I want  
> to run an amber minimization with a better parameter set. However,  
> the mol2 files are not like pdb files and do not come with atom  
> types for amber calculations. Is there anyway to (auto?)assign  
> amber atom types to the atoms in my file so your program can run a  
> calculation? Thank you.
>        -Pasquale Iacono, B.S.
>         Ithaca.College

More information about the Chimera-users mailing list