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 http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html 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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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