On Thu, Mar 24, 2016, hannes.loeffler.stfc.ac.uk wrote:
> The atom "names" are just arbitrary string labels. Many codes rely on
> this to uniquely identify atoms but that is really a rather dumb way
> of doing this. Antechamber will probably just simply construct those
> labels combining the element name with a running counter.
Not really true: antechamber respects the atom names in the input pdb file.
I suspect that your pdb file had atom names in the wrong columns, so that
several atoms ended up with the same name (as read by antechamber). In that
case (and that case only) antechamber will disambiguate the names by adding
numbers after that input name.
Aside: not at all sure whay using atom names is "dumb". In any event (as
Hannes notes) it is a common practice in many codes.
...dac
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Received on Thu Mar 24 2016 - 04:30:03 PDT
