> 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.
There exists no rule that allows a 1-to-1 mapping of all possible atom types to all possible 4-letter(?) atom names in such a way that a human can readily remember the mapping. Thus whatever rule you do use has a shortcoming. >> 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. I didn't say to use a PDB file... I said life is easier if you can assume the PDB *naming convention*. However, you might just as easily use editconf as a filter to convert .gro to .pdb and feed that to your visualization program, if the atom-name-to-atomic-number mapping already works there. >> 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. VMD and ngmx both do this already... Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
