From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Jan 20 2012 - 18:41:27 CST
Dear NAMD developers,
I am just curious to know whether the SASA-proportional hydrophobic energy
term for implicit solvent simulations is available in one of the nightly
builds of NAMD.
Thanks!
Gianluca
On Thu, 13 Oct 2011, David Tanner wrote:
> 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.
>
> ...
>
> 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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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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