Hi Nikolay, The columns are the atom *name* and the atom *type*. The one before the coordinates is the name. I don't know what you mean by "compatible," are you trying to use the Mol2 file as input to one of the Amber-suite programs? As you saw, there is an option in the Mol2 saving dialog to write Amber/GAFF types instead of SYBYL types. There is no option for Amber atom names. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2> I don't know if the Mol2 file with Amber/GAFF types is intended as input to another program. It is not intended as input back into Chimera. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 24, 2012, at 9:42 AM, Nikolay Igorovich Rodionov wrote:
Hi all, Simple Questions: To create mol2 files with naming compatible with Ambersuite programs I would have to save with non-sybyl hydrogen naming, yes? Also, after I save the files with the amber style naming scheme, which atom name column has the AMBER style naming (there are two)? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015