> This has always been a real pain in things like QM/MM where one needs to know the atomic number but that
> information does not reliably exist.
Why not use the atomic numbers listed in the library file? I mean, each atom type does correspond to a unique element. You just need to know what that is, and that information is right there in the file (aside from the ones that say -1, which is just a bug).
> The routine I use in the QM/MM code is to take the Atom name (from the PDB file that gets processed into the prmtop
> file) and then pull the first letter of this and then try to essentially figure out the element based on that and the mass.
Yes, I've done the same thing on occasion, but as you say it's hard to do reliably. For example, CL means chlorine, not carbon, but CA means carbon, not calcium.
Peter
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 04 2011 - 10:30:07 PDT
