> > 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.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Oct 04 2011 - 11:00:08 PDT
