From: Jason Swails (jason.swails_at_gmail.com)
Date: Mon Apr 14 2014 - 07:31:05 CDT
On Mon, 2014-04-14 at 13:23 +0400, James Starlight wrote:
> And some additional questions:
> 1 ) In MMPBSA.py manual I've found that for this script four topology
> files should be provided besides the input file:
> -sp solvated_prmtop \ -cp complex_prmtop \ -rp receptor_prmtop \ -lp
> should this files be taken from the param files provided in the namd
> files as you can see below or alternatively obtained from the resulted
> psf ?
> parameters ../parameters/par_all27_prot_lipid.inp
> parameters ../parameters/ligand.prm
> parameters ../parameters/water_ions.prm
You need to use "chamber" to combine the parameter files and PSF files
into an Amber-style topology file that MMPBSA.py will understand. In
AmberTools 13, chamber supports only a single "parameter" file, but if
you pretend the additional parameter files are "stream" files then
chamber should work fine.
> 2) What difference in resulted dG should be expected between
> calculations in (PB) or (GB) regimes assuming that I'll try to
> estimate free energy of the binding hydrophobic ligands (contribution
> from the polar interactions of only up to 30%) to the membrane
> receptors ?
That depends on your system. You'll have to try it to find out. Vlad
made very good points in his email about trusting defaults and taking
care with the parameters you use. MM/PBSA is an advanced technique and
I would recommend doing a literature review to see how to compute
binding free energies most reliably.
Hope this helps,
-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher
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