RE: Binding free energy of a protein complex

From: Gadi Oron (
Date: Wed May 05 2004 - 09:31:52 CDT


Thank you for your help.

The problem is that your script calculate the interaction energy, and
not the FREE energy, which is different since it involves the entropy.

BTW, I believe that you can ask NAMD to calculate the interaction energy
directly using the pairInteraction directive like this:

1. Do a normal run
2. Create a PDB with beta=1 or 2 for the parts you wish to calculate
3. Use the following code in your namd config:

# Atom in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction on
pairInteractionFile pair_tmp.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2

set ts 0
coorfile open dcd out/run.dcd

# Read all frames until nonzero is returned.
while { ![coorfile read] } {
  # Set firstTimestep so our energy output has the correct TS.
  firstTimestep $ts
  # Compute energies and forces, but don't try to move the atoms.
  run 0
  incr ts 1
coorfile close

NAMD will dump the interaction energy for each frame in the DCD file,
but again, it is not the free energy.

On Mon, 2004-05-03 at 14:02, Ahmet Bakan wrote:
> Hi Gadi and All,
> I have attached a script, which calculates the electrostatic, vdW, and
> Hbonding energy of a protein complex within a CutOff distance.
> Works like this:
> You get
> #OfPairsWithinCutOffDistance ElectEnergy vdWEnergy #OfHBonds HbondEnergy
> And a file of list of above interactions for all pairs.
> Could you tell me your ideas on the script? I would like to develop it to
> get a better measure of binding energy.


================= Gadi ORON, PhD -o- Proteologics ======================
========== gadi/at/ ========== +972 8 9475666 ==========
I can't think about that.  It doesn't go with HEDGES in the shape of
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