From: somedatta pal (somedatta.pal_at_gmail.com)
Date: Tue Mar 19 2013 - 00:35:22 CDT
On 3/19/13, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Tue, Mar 19, 2013 at 5:58 AM, somedatta pal <somedatta.pal_at_gmail.com>
> wrote:
>> Hi,
>> I am studying effect of protein's charge and flexibility on its
>> stability, structure and function. With this aim, i want to observe
>> the case when protein-water interaction is turned off, but
>> protein-protein and water-water interactions are turned on. Can anyone
>> please help me?
>
> what would be the point of this kind of calculation? if there are no
> protein-water interactions, you could just simulate the protein in
> vacuum, i.e.without any water present, and the water without a protein
> as well.
>
> axel.
>
>
>>
>> --
>> Somedatta Pal
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
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.
Somedatta ..
I.I.T. Kgp,
India
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