Re: Solvation free energy calculation with MM/GBSA

From: Jeff Comer (
Date: Thu Sep 24 2015 - 08:27:26 CDT

Dear Neelanjana,

NAMD will do these calculations. For an example of where this was
done, see:

Remove water and ions from your dcd file (for example, using VMD) and
then run your dcd through NAMD with generalized Born implicit solvent
turned on. See the excerpt from a configuration file below. You can
then extract the potential energy from the NAMD log file (which is
your GBSA free energy).

If you use the single trajectory scheme, you'll convert your explicit
solvent dcd into 3 new dcd files. To get protein–ligand binding energy
(or in your case, protein–nanosurface), you (1) delete everything in
the dcd but the protein, (2) delete everything but the ligand, and (3)
delete just the water and ions around the protein and ligand. You then
extract the potential energy from the dcd file and get ΔG_bind = <
G_GBSA(3) – G_GBSA(2) – G_GBSA(1) >, where the average is over all
frames of the dcd.


# implicit solvent
gbis on
solventDielectric 78.5
ionConcentration 0.3
alphaCutoff 15
sasa on
surfaceTension 0.00542

# nonbonded parameters
switching on
switchDist 15
cutoff 16
pairListDist 18

set ts 0

foreach dcd $dcdList {
    coorfile open dcd $dcd
    while { ![coorfile read] } {
    firstTimestep $ts
    run 0
    incr ts 1
    coorfile close

Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Sep 23, 2015 at 6:51 AM, Neelanjana Sengupta
<> wrote:
> Dear NAMD community,
> We would like to calculate the solvation free energy, using the Generalised
> Born Surface Area (MM-GBSA) method, of a protein-nanosurface system that has
> been simulated with NAMD; we have the PSF file and the DCD files.
> Could you suggest how to go about this? (The APBS method will only allow the
> PBSA method).
> We are investigating options where we convert our trajectories to the AMBER
> format and use the utilities available there, but this is very messy...
> Thanks in advance.
> Regards,
> Neelanjana

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