Also, keep in mind that unless you've done some kind of analysis to
determine how converged your results are, any peaks you see may not be
meaningful. 20 ns may or may not be enough time to converge your
system. One way to approach this is to calculate your energies using
only the first half of your data, then add more and more data to see
how your results change. Once they stop changing significantly you can
have more confidence in your results.
-Dan
On Wed, Mar 9, 2016 at 5:41 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 09 2016 - 08:00:06 PST
