On Tue, Oct 4, 2011 at 1:44 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> > > 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).
>
> Because library files never make it out of Leap. I.e. to run a simulation
> one only needs a prmtop, inpcrd and mdin file and the atomic number are not
> in the prmtop file. Now perhaps given prmtop files are now extensible they
> should be updated to include the atomic number in case someone wants to run
> QMMM simulations but this would mean updating XYZ,G,S leap as well to write
> this information and have sander look to see if it is there and fall back
> to
> the current method if it isn't. I just have never found the time to go and
> do this and as you say the -1 bug makes it pretty useless until that is
> first fixed. At some point I probably started to do this, found the -1 and
> just gave up and figured I didn't have the time to follow it all through
> and
> sort out the mess.
>
But the -1 is fixed now :). In any case, I had thought about adding an
ELEMENTS section to the topology file, but that will have to wait for some
of my other projects to progress more.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 11:00:10 PDT
