[MMTK] PDB producing, amber_atom_charges

Konstantinos Makrodimitris kmakr7 at msn.com
Wed May 28 15:07:43 EDT 2003


Hi,

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.
For example in the simple case of aminoacids one could find PDBs but
you must try by yourself to put specific namespaces(H_beta,HB1 etc)
by hand in order to don't be incosistent and take errors with PDB reading 
functions in MMTK.
Of course the other way is to go to Protein Data Bank but nowing the PDB ID 
etc
however I need a more custom build especially with protected groups
something like a utility that does that automatically with rules a website 
etc.



I noticed also in the documentation of Database construction and in the 
respective files
that is defined  the dictionary "amber_atom_type" defines the atom type for 
each atom; the dictionary "amber_charge" defines the partial charges.
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?


Best,
Kon

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