[MMTK] Weird energy evaluation

[Ioannis Ioannidis]

Hi again,

I want to get the atom coordinates for all the peptides from pdb files.
The purpose is to get the interaction energies between all the peptide
pairs and the energy of each individual residue. I used the following
program

from MMTK.PDB import PDBConfiguration
from MMTK import InfiniteUniverse
from MMTK.ForceFields import Amber94ForceField

universe=InfiniteUniverse(Amber94ForceField())
configuration=PDBConfiguration('glu.pdb')
m=configuration.createAll()
universe.addObject(m)
print universe.energy(m)

to get the energy of glutamine, where the pdb file was

ATOM     10  C   GLU     1       0.551  -1.198  -0.766  1.00 33.00      AUTO
ATOM     11  N   GLU     1      -1.458   0.000   0.000  1.00 33.00      AUTO
REMARK ATOM     12  HN  GLU     1      -1.871   0.808   0.419  1.00  0.00      AUTO
ATOM     13  O   GLU     1       0.024  -2.306  -0.667  1.00 33.00      AUTO
ATOM     14  CA  GLU     1       0.000   0.000   0.000  1.00 33.00      AUTO
ATOM     15  CB  GLU     1       0.536   0.000   1.433  1.00 33.00      AUTO
ATOM     16  CD  GLU     1       0.791   1.240   3.618  1.00 33.00      AUTO
ATOM     17  OE1 GLU     1       1.225   0.156   4.060  1.00 33.00      AUTO
ATOM     18  OE2 GLU     1       0.785   2.297   4.285  1.00 33.00      AUTO
ATOM     19  CG  GLU     1       0.246   1.278   2.204  1.00 33.00      AUTO
ATOM     23  HA  GLU     1       0.336   0.917  -0.507  1.00 33.00      AUTO H
ATOM     24  HB2 GLU     1       0.099  -0.851   1.977  1.00 33.00      AUTO H
ATOM     25  HB1 GLU     1       1.624  -0.160   1.406  1.00 33.00      AUTO H
ATOM     26  HG2 GLU     1       0.685   2.133   1.668  1.00 33.00      AUTO H
ATOM     27  HG1 GLU     1      -0.841   1.443   2.238  1.00 33.00      AUTO H

I had to remove the second entry because MMTK didn't have an entry for HN
in its database entry for glutamine. What troubles me is that the energy
returned is negative (approximately -213). Isn't energy supposed to be
positive? I'm getting the same with most of the other residues.

Thanks
Yannis