[Chimera-users] Amber-style mol2 name

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 25 08:52:31 PDT 2012


Well, there are exceptions to everything, but generally:

Atom types define what parameters are assigned to the atom in various calculations.  Often there will be many atoms in a residue that have the same type, but they could have different names... For example, in this Mol2 file, every atom has a unique name, but all of the hydrogens are type H, two carbons are type C.2, and the remaining carbons are type C.3.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/example.mol2in>  

Some formats or programs require unique atom names in a residue so that each atom can be specified uniquely, but some do not have this requirement.

Different programs have different atom-naming rules, and these atom names might or might not imply the types of the atoms.

Different programs use different sets of types, and you have to look at the documentation for that program to see a description of the types.

If you want more perspectives on these concepts, you could try asking on ccl.net.
Best,
Elaine
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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 25, 2012, at 3:14 AM, Nikolay Igorovich Rodionov wrote:

> 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?




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