Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact?

From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Wed Mar 20 2013 - 08:45:51 CDT

Hi Somedatta,

I could be wrong, but I think this should be possible using the Alchemical
FEP tool. Usually this tool is used to gradually turn off interactions
between a ligand and a protein, using a coupling parameter lambda, but you
could just do the simulation using one value of the coupling parameter
which corresponded to the interactions you wanted. You can turn off VDW and
electrostatics separately using this tool. Then, of course, your "ligand"
would be all of the waters in the system ; the developers could tell you
whether it would be computationally prohibitive.

In any case, if you are looking to modify the code, my guess is that much
of the work is already done as part of the FEP module, and may just need
slight tweaks.

cheers,
Grace

On Wed, Mar 20, 2013 at 3:47 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> I guess there's currently no way how to do that with namd. You would have
> to
> implement it by yourself. Additionally, you could just compute the
> electrostatic potential instead of sampling over varying configurations to
> see what's happening, or?
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von somedatta pal
> > Gesendet: Mittwoch, 20. März 2013 06:37
> > An: Norman Geist; namd-l
> > Betreff: Re: namd-l: Can protein-water electrostatic interaction be
> > turned off keeping protein-protein (vdw+elect) and water-water
> > (vdw+elect) interactions intact?
> >
> > Hi,
> > Thanx for your reply. Without PME, if I use a cutoff value, then
> > vdw and electrostatic interactions will be calculated within this
> > distance for all the atoms. But I want to turn off the protein-water
> > electrostatic interaction completely. Other interactions, like
> > protein-water vdw
> > interactions, protein-protein (elect+vdw) interactions, water-water
> > (elect+vdw) interactions
> > should be intact. Is their any option in NAMD for performing
> > simulation in such a way?
> > I am looking forward for your kind reply.
> >
> > On 3/19/13, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
> > > Hi,
> > >
> > > without PME you will have turned off long range electrostatics. Now
> > you can
> > > control the range of vdw and short range electrostatics by changing
> > the
> > > cutoff value.
> > >
> > > Norman Geist.
> > >
> > >> -----Ursprüngliche Nachricht-----
> > >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > >> Auftrag von somedatta pal
> > >> Gesendet: Dienstag, 19. März 2013 08:55
> > >> An: namd-l
> > >> Betreff: Fwd: namd-l: Can protein-water interaction be turned off
> > >> keeping protein-protein and water-water interactions intact?
> > >>
> > >> ---------- Forwarded message ----------
> > >> From: somedatta pal <somedatta.pal_at_gmail.com>
> > >> Date: Tue, 19 Mar 2013 13:15:15 +0530
> > >> Subject: Re: namd-l: Can protein-water interaction be turned off
> > >> keeping protein-protein and water-water interactions intact?
> > >> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > >>
> > >> On 3/19/13, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> > >> >> Hi,
> > >> >> I want to study how the microscopic stuctural and dynamic
> > >> properties of
> > >> >> water
> > >> >> molecules present in the vicinity of a protein are expected to be
> > >> >> sensitive to its local conformational motions and the presence
> > >> >> of polar and charged groups at the surface capable of anchoring
> > >> >> water molecules through hydrogen bonds. For this purpose, I
> > >> performed
> > >> >> 3 simulations:
> > >> >> (a) The fully flexible protein molecule
> > >> >> in equilibrium with the solvent.
> > >> >> (b) the protein molecule was kept frozen but in equilibrium with
> > >> solvent.
> > >> >> (c) The protein molecule was kept frozen and the electrostatic
> > >> >> interactions between the protein and the water molecules were
> > turned
> > >> >> off.
> > >> >> In case (c), I made the charge of all the protein atoms zero.
> > Thus
> > >> >> not only protein-water electrostatic interaction is zero, but
> > also
> > >> the
> > >> >> protein-protein electrostatic interactions are also become zero.
> > >> >>
> > >> >> But i want to perform one simulation where protein-water
> > >> >> interactions (vdw+electrostatic) will be zero, but protein-
> > protein
> > >> >> interactions remain unchanged.
> > >> >> I am waiting for your kind reply.
> > >> >
> > >> > you don't have to repeat what you already wrote. it doesn't make
> > any
> > >> > difference, since i already *told* you: what you describe is
> > >> > simulating the protein in vacuum! if there are no protein-water
> > >> > interactions, then it doesn't matter whether there are water
> > >> molecules
> > >> > present at all. case closed.
> > >> >
> > >> > axel.
> > >> >
> > >>
> > >> Hi,
> > >>
> > >> I want to study a case when the long-range electrostatic
> > inateraction
> > >> between protein and water should be turned off, but short range vdw
> > >> interaction between protein and water will be intact. And
> > >> protein-protein and water-water interactions (vdw+electrostatic)
> > >> should be unchanged. Can you please give any idea, how this can be
> > >> done?
> > >> >
> > >> >
> > >> >>
> > >> >> Somedatta ..
> > >> >> I.I.T. Kgp,
> > >> >> India
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > >> > International Centre for Theoretical Physics, Trieste. Italy.
> > >> >
> > >>
> > >>
> > >> --
> > >> Somedatta Pal
> > >>
> > >>
> > >>
> > >> --
> > >> Somedatta Pal
> > >
> > >
> >
> >
> > --
> > Somedatta Pal
>
>
>

-- 
Grace Brannigan, Ph.D.
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ
(856)225-6780
www.branniganlab.org

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:02 CST