[Chimera-users] Amber-style mol2 name

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 24 09:55:32 PDT 2012


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




More information about the Chimera-users mailing list