On Wed, Mar 9, 2016 at 3:26 AM, Zhang Marc <marczhang_md.zoho.com> wrote:
> Hi Jason
>
>
>
> Thanks a lot for your explanation.
>
>
>
> The non-polar interaction I refereed is the value of van der waals
> component.
>
>
>
> The result show van der waals= -1.21 that could be difficult to
> understand, as Threonine is a polar residue.
>
>
>
> I do not know how it contributes to the van der waals interaction.
>
As Carlos pointed out, every atom (except hydroxyl hydrogens) has van der
Waals parameters. At distances larger than Rmin, the van der Waals
interactions are always favorable and their energies negative. For highly
charged and polar systems -- like water -- the electrostatic attraction
forces particles close together, and the vdW term can become positive.
However, for interactions that do *not* have a strong electrostatic
component, the structure is held together by vdW interactions, and so they
are typically negative. Since MM/PBSA gets rid of explicit water, the vdW
interactions between the atoms will usually be negative. Since the bound
state has *more* of these contacts (since they exist between the receptor
and ligand, whereas the unbound state does *not* have these receptor-ligand
interactions), the total vdW energies in the unbound state will be larger
than that in the bound state (because there will be fewer of those
interactions). This will be distributed over all residues in the receptor,
with those residues *closest* to the active site having more negative
values for vdW than those farther away.
Keep in mind that force fields are incredibly simple concepts. The common
ones don't know anything about chemistry, like "hydrophobic" vs.
"hydrophilic" interactions, or hydrogen bonding, or polar vs. nonpolar
interactions, etc. These concepts you learn in biochemistry class can be
rationalized based on the results of a calculation but it is not always
that straightforward.
HTH,
Jason
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Received on Wed Mar 09 2016 - 05:00:04 PST
