Re: [AMBER] Simulation of the protein with internal water

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 05 Jun 2014 19:04:21 -0700

TIP3 waters have a spherical vdw centered on the O and containing
the H's. In solute-ion/water-ion parameterization we found that
we needed to paramterize the ion radii differently depending on
whether they were in solvent or solute. The same may apply to
parameterization of water in solute vs. solvent. Though I don't
recall any discussion of the issue.

    Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
    Perturbation Studies. W.S. Ross and C.C. Hardin
    Journal of the American Chemical Society 116, 6070 (1994).


James Starlight <> wrote:

> Dear Amber users!
> I've performed some equilibration simulation of my water-soluble protein
> having internal cavity permeable for the solvent water. Foe the trajectory
> analysis I've noticed that several water have been moved inside the protein
> and made hydrogen bonds with the polar side chains. Now I've selected my
> protein with these internal waters in the separate pdb and would like to
> resolvate this system and perform new simulation. My questions.
> 1) Does it possible to keep internal water within my protein with this new
> model? How I should define internal water (as the ligand for instance )?
> 2) More general question. What model for solvent water should be used
> better for modelling permeation of the solvent within protein?
> TFH,
> James
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Received on Thu Jun 05 2014 - 19:30:02 PDT
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