[MMTK] PDB producing, amber_atom_charges

[Konrad Hinsen]

> I'd like to ask your advice for producing easy and not by hand PDBs for
> aminoacids,
> proteins, peptides with protected groups in a way to be consistent to
> PDB naming conventions for atoms in proteins and to MMTK utility of course.

From what kind of input information would you like to create such PDB files?

> Eg for alanine residue:
> >>>ii.amber_charge
>
> {<Atom number 9>: 0.060299999999999999, <Atom number 8>:
> 0.060299999999999999, <Atom number 7>: 0.060299999999999999, <Atom number
> 6>: -0.1825, <Atom number 5>: -0.56789999999999996, <Atom number 4>:
> -0.41570000000000001, <Atom number 3>: 0.082299999999999998, <Atom number
> 2>: 0.27189999999999998, <Atom number 1>: 0.033700000000000001, <Atom
> number 0>: 0.59730000000000005}
>
> >>>ii.amber_charge.keys()
>
> [<Atom number 9>, <Atom number 8>, <Atom number 7>, <Atom number 6>, <Atom
> number 5>, <Atom number 4>, <Atom number 3>, <Atom number 2>, <Atom number
> 1>, <Atom number 0>]
> But how could I index with a key to take the respective value
> I would need eg ii.amber_charge['key?']=0.060299999999999999
> Could I index in a way to take eg only the sidechains charges?

Here is an example for a water molecule:

  w = Molecule('water')
  print w.getAtomProperty(w.H1, 'amber_charge')

This is how MMTK accesses these tables as well internally.

Konrad.
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