AMBER Archive (2007)

Subject: Re: AMBER: regarding implicit simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Aug 14 2007 - 06:22:24 CDT

if the protein requires a specific hydrogen bond to a structured
water and you do not have it, then the behavior will be different.
this is a limitation of continuum solvent models.
Of course just because a water is localized in for example a
crystal structure, it does not mean that the structure of the water
is important to the protein.

On 8/14/07, gurpreet singh <gps.iitm_at_gmail.com> wrote:
> Hello Users
> i have a general question on implicit simulation method. I will ask with
> an example, say a protein needs one water molecule to be present at a
> particular point for it to behave normally during the simulation.
> Now in implicit simulation since we are not having any water as such but we
> are using the dielectric constant similar to water, my question is, will the
> simulation in such solvent will give us the same structural changes as we
> were expecting .
>
> Although i know that in general that much difference in the movement will be
> there if we compare explicit and implicit but i want the answer with respect
> to the above example.
>
> I hope my question is clear.
>
> Thanks & Regards
> Gurpreet
> IIT MADRAS
> INDIA
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