Re: AMBER: nonpolar solvation energy

From: Carlos Simmerling <>
Date: Wed, 31 Jan 2007 14:54:14 -0500

keep in mind that if you do this with water, you'll likely need a much
smaller surface
tension term to estimate the hydrophobic contribution to solvation. Most
the SASA term attempts to account for the _difference_ between the
and the solute-solvent vdW terms, resulting in a small surface tension.
If you
directly calculate the dispersion term then you need a larger surface
It's not something to try unless you understand these issues well.

Ray Luo wrote:
> You can definitely compute solute-solvent vdw interactions by running MD in
> TIP3P/PME. This is exactly how the nonpolar solvent in amber9 was calibrated
> in the first place. However, you need:
> 1) Run MD for each MMPBSA snapshot with all solute atoms restrained.
> 2) Make sure all above runs are fully equilibrated. You can check the
> quality of equilibration to looking at the running average of vdw energy for
> each of the runs.
> 3) Once you are sure the MD runs are fully equilibrated, you need to use
> ptraj to generate at least 100 inpcrd files (fully uncorrelated, i.e. at
> least 5ps apart) in the equilibrated portion of the trajectory for each
> MMPBSA snapshot. You need three set of inpcrd files for each MMPBSA
> snapshot, one for solute/solvent, one for solute only, and one for solvent
> only.
> 4) Then you compute mean vdw energies for the three sets for each MMPBSA
> snapshot. AND you have to change the sander program to make sure that you
> only compute the attractive portion of the vdw energy. This attractive
> portion of the vdw energy is what you need in MMBPSA using the new nonpolar
> solvent model.
> 5) Finally use <U(solut_solv)> = <U(total) - U(solut) - U(solv)> to compute
> the needed solute/solvent vdw energy for each MMPBSA snapshot.
> Finally you can go back to your usual MMDPBSA calculation. So the bottom
> line is that it is extremely involving and I strongly recommend that you
> upgrade to amber9 to use the new PBSA for this.
> All the best,
> Ray
> ==========================================
> Ray Luo, Ph.D.
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900
> Phone: (949) 824-9528
> Email:
> Web:
> ==========================================
> hi all
> i have a question regarding MMPBSA in amber8
> since the program doesnt calculate the solute-solvent
> vdW interaction or the dispersion contribution as
> regard to the nonpolar solvation energy, is there any
> way that i could do it manually? my knowledge is quite
> limited, can i do it by running sander in explicit
> solvent for each extracted snapshot and just take the
> vdW contribution? but the values would be so huge, is
> that correct? because it would involve solvent-solvent
> interaction as well (is it?) and how many steps should
> i run? is it enough if just 1 step? i really need
> someone to guide me on this
> i know that in amber9, the dispersion contribution has
> been implemented in PBSA, thats really neat but i dont
> have amber9.
> if there are other suggestions on how i should extract
> the solute-solvent vdW contributions, please shout
> out, i would definitely definitely appreciate it very
> very much!
> thanks all
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Received on Sun Feb 04 2007 - 06:07:14 PST
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