On Thu, 24 Mar 2016 07:16:23 -0400
David A Case <david.case.rutgers.edu> wrote:
> 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.
What I mean is that it would not be very clever when a code solely
relied on atom labels for unique identification. This is essentially a
matter of trusting the input to be "correctly" formatted. A big
problem for robust codes and automatisation in particular.
But what I want to say in regards to the case here is that the atom
labels in the mol2 file should not have any further consequences. I
would expect, I haven't checked this, that the mol2 reader would only
record those names but not use it for anything beyond. All that
matters for topology creation (and coordinate conversion) is that a
certain atom index has a known atom type, a charge and coordinates.
The mol2 file is, after all, its own templats (ok, a frcmod may be
needed too).
Cheers,
Hannes.
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Received on Thu Mar 24 2016 - 07:30:03 PDT
