RE: Binding free energy of a protein complex

From: Gadi Oron (gadi_at_proteologics.com)
Date: Wed May 05 2004 - 09:31:52 CDT

Hi,

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:
> HBONDING 3.2
> 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.

Ciao

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