[gmx-users] atomname -> atomic number

[David van der Spoel]

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? 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.
> 
> 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.

This has been implemented for pdb files. For gro files this is useless.


> 
> Mark
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se