[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.

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.
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

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