[MMTK] Several questions

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Tue, 20 Nov 2001 17:26:23 +0100

Hi Konrad,

thank you for your answer. I did not understand everything and would
to ask more questions about it.

> That is right. The idea is that a higher-level object definition can
> override the parameters defined in its elements. For example, you can
> predefine default charges for a methyl group, but still decide on
> different charges for a specific molecule that contains a methyl
> group.

do you mean by higher-level object definition? Is is the charge in the
file or the individually defined charge defined by "atom.amber_charge"?
it be logical, if the individual charge definition for an atom overrode
the default
charge from the definition file? In your example with the methyl group,
it would mean
that when you assign "amber_charge" to an atom, this value would be
used, and if the
atom did not get a special charge, the default value out of the
definition file is
used. At the moment, you would have to create a new definition file
without charges in 
order to assign individual charges.

What have I misunderstood here?

I have another question concerning the output into a PDB file. In which
order are the atoms within a residue/molecule written out? I noticed
that the PDB output has the same order as the atoms are listed in
"res.pdbmap", where "res" is an amino acid residue. Is it indeed
determined by that and where? I could only understand that the attribute
"pdbmap" is created in the module "Biopolymers._init(self)" out of the
pdbmaps for the peptide and sidechain parts. Then I don't understand,
why atoms belonging to the peptide or sidechain part are mixed in the
order in "res.pdbmap" (e.g. in alanine). So how is the order determined?
I assume that for a given residue the output order of the atoms is
always the same?

I am also wondering about one thing with the AMBER force field and
couldn't find an answer at their homepage. When you have the dihedral
parameters, e.g.

X -CT-N -X    6    0.00          0.0             2.        

then i=6 the number of paths, V/2=0.00 some sort of amplitude ,
gamma=0.0 the offset and n=2 the periodicity. The energy contribution is
(phi is the angle)
V/2i*(1+cos(n*phi-gamma)). If V=0, how can this term give an energy
contribution? And if it doesn't, why do they list it (I tried removing
it and it made a difference in energy)?

Thanks a lot,

Berit Hinnemann
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark 
Phone: +45 4525 3209, Fax: +45 4593 2399