Hi Peter,
> More seriously though, I'm porting the AMBER force fields to work with
> a different MD code (OpenMM), and for that purpose I do need to know
> the element of each atom type. This same issue also comes up in
> all_amino03.lib, and possibly others I haven't come across yet.
The problem is that the element is never actually defined or used in the
AMBER force field. It is purely based on atom type which in turn gives the
atomic mass through the parameter files. 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. 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. You can take a look at
the routine 'get_atomic_number' in
$AMBERHOME/AmberTools/src/sqm/qmmm_module.f but it is far from perfect.
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 - 10:30:06 PDT
