[Chimera-users] Amber-style mol2 name

Nikolay Igorovich Rodionov nirodion at syr.edu
Thu Oct 25 03:14:06 PDT 2012


Would you mind elaborating about the differences between atom types and
atom names? I thought they were essential one in the same; looking at a
generic mol2 file, it seems like every atom name has a unique atom type.
What differentiates them?

Thanks!

Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015
Martin J. Whitman School of Management & L.C. Smith College of Engineering
at Syracuse University

Syracuse, New York 13244
Phone: 281.301.9401| Email: Nirodion at syr.edu







On 10/24/12 6:00 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

>Sorry, there is no option in Chimera to rename your atoms with Amber
>names. Looks like the PDB2PQR server might be able to do it:
>
><http://nbcr-222.ucsd.edu/pdb2pqr_1.8/>
>
>I haven't tried it, though.  If it works, you could read the resulting
>PQR into Chimera and then write Mol2.
>Elaine





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