Re: GBIS and hydrophobic solvation

From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Thu Oct 13 2011 - 13:40:32 CDT

NAMD Implicit Solvent users,

Though NAMD's implementation of implicit solvent does not currently include
a SASA-proportional hydrophobic energy term, I believe one will be available
early 2012.

As for the questions "What can be accurately modeled with an implicit
solvent which screens electrostatics but doesn't account for the non-polar
effect of solvent?" - this is an excellent question for which I don't have a
good answer. Once the hydrophobic energy term is available in NAMD, I will
explore what effect it has on protein structure.

Thank you,
David E. Tanner

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Mon, Oct 10, 2011 at 10:11 AM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:

> **
> One additional connected question, to obtain more complete answer in whole
> . I was used GBIS in NAMD 2.8 for implicit solvation in EtOH, to this point
> (because of short alkyl chain in alcohol) lack of hydrophobic term should
> not be a problem. But solvated (small organic molecules) are hydrophobic in
> significant extent (and very soluble in EtOH in reality). So if there is
> really lack of hydrophobic term in GBIS, as implemented in NAMD, did I
> obtained reliable results?
> Thanks
>
> Branko
>
>
>
>
> On 10/10/2011 2:24 PM, Jérôme Hénin wrote:
>
> Hi everyone,
>
> I have just read the very interesting paper that describes how
> Generalized Born Implicit Solvent was parallelized in NAMD.[1] A
> well-known limitation of GBIS is that it does not describe hydrophobic
> solvation or the hydrophobic effect in water. That effect is of course
> pretty important for protein conformation, and completely central to
> anything involving membranes. That's why some implementations of GBIS
> are augmented with empirical nonpolar solvation terms (e.g. [2]),
> which NAMD does not have so far [3], although it implements the method
> of Onufriev et al. who did use such a term in their work [4].
>
> Given these circumstances, what classes of problems is NAMD/GBIS
> well-suited for?
>
> Thanks for your input,
> Jerome
>
>
> [1] http://pubs.acs.org/doi/abs/10.1021/ct200563j
> [2] http://onlinelibrary.wiley.com/doi/10.1002/jcc.21813/abstract
> [3] http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13710.html
> [4] http://onlinelibrary.wiley.com/doi/10.1002/prot.20033/full
>
>
>
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