From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Fri Sep 25 2015 - 07:36:50 CDT
Dear Jeff,
Thank you very much for the script and the reference! We are indeed getting
very reasonable solvation free energies with this procedure!
Cheers,
Neelanjana
On Thu, Sep 24, 2015 at 6:57 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Dear Neelanjana,
>
> NAMD will do these calculations. For an example of where this was
> done, see: http://dx.doi.org/10.1021/jp4000363
>
> 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.
>
> Regards,
> Jeff
>
> # 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
> <senguptan_at_gmail.com> 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
>
-- ~~~~~~~~~~~~~~~~~~~~ Neelanjana Sengupta, PhD Physical Chemistry Division National Chemical Laboratory Dr. Homi Bhaba Road Pune 411008, India Phone: +91-20-2590 2087 Fax: +91-20-2590 2636 URL: http://academic.ncl.res.in/n.sengupta ~~~~~~~~~~~~~~~~~~~~
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