Re: GBIS and hydrophobic solvation

From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Wed Feb 15 2012 - 15:36:31 CST

Not yet; it may be available in March or April.

Thank you,
David E. Tanner

On Fri, Jan 20, 2012 at 6:41 PM, Gianluca Interlandi
<gianluca_at_u.washington.edu> wrote:
> 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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