[MMTK] Questions on adding a displacement to the co-ordinates of a Protein

vanitha at cs.wisc.edu vanitha at cs.wisc.edu
Mon Nov 28 22:59:06 CET 2005

Sorry for the spate of emails...

I am attempting to compute the energy and gradients of a given protein,
and then add a small displacement to the co-ordinates of the protein and
evaluate it's energy and gradients at the new co-ordinates.

I have questions related to this issue:

1) When I try to print the configuration of a protein in a universe, I get
the result <MMTK.ParticleProperties.ParticleScalar instance at 0xb71770ac>
How can I print the vector of co-ordinates of the Protein? I'm a MATLAB
person, so I'm comfortable thinking in terms of vectors and matrices. Can
somebody shed light on how to do this in MMTK?

Here is the code that attempts to do what I described above:

from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField

universe = InfiniteUniverse(Amber94ForceField())
universe.Protein = Protein('1bp2.pdb')

# Compute the energy and gradients of the protein
energy, gradients = universe.energyAndGradients()
print energy

# Get the co-ordinates of the protein
configuration = universe.configuration()

# This line does not do what I'm expecting it to!
print configuration.length()

2) Can I use the universe.addToConfiguration(some particle vector) method
to add a displacement to the current configuration?

3) Can I add two proteins to a universe? This is probably a dumb
question... but is this equivalent to doing a co-oridinate transformation
of one of the proteins to bring it into the same reference frame as the
other protein?

4) Another related question... Can I add a ligand and receptor to the same
universe and compute the energy and gradients for the resulting pair? If
so, how can I update the displacements of the individual proteins?

Thanks in advance,

- Vanitha

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