[gmx-users] atomname -> atomic number

[Daniel Baum]

Mark Abraham wrote:
> Daniel Baum wrote:
>> Hi,
>>
>> I would like to write a reader for *.gro files, but I couldn't find any
>> information about how to map the atomname to the atomic number. Can
>> anyone shed some light on this problem? I would be most grateful.
>
> It's an ill-defined problem... is "HG" mercury or some kind of
> hydrogen? "CD" a delta-carbon or cadmium?
Right, but I'd like to know.  Is it really like this?  Can exactly the
same atomname really have different meanings?  That's bizarre.  There
should be some rule, shouldn't there.
> It's better-defined if you can assume some kind of convention about
> atom naming, e.g. the PDB one, or the NMR one, etc.
I know that PDB is well-defined, but this doesn't help because I want to
read .gro files.
> It's much easier to avoid re-inventing the wheel. People may have some
> suggestions if you let us know why you want to write a .gro reader
> that needs to assign atomic numbers.
I don't want to re-invent the wheel.  I simply have some .gro files and
I want to know the element type in order to display the atoms correctly
according to their element type/atomic number.

    Daniel