[Chimera-users] Using mol2 files
meng at cgl.ucsf.edu
Tue Jul 3 15:30:12 PDT 2007
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
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.
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