[gmx-users] Bulk waters placed inside protein core

[Anton Feenstra]

Choon Peng wrote:

> Hi Daan,
> 
>   Thank you for the reply.
> 
> Sorry, I forgot to mention that I've kept the crystal waters.
> I used to delete them with I first started doing MD but later realized
> their importance.
> 
> Actually, we wish to investigate whether the buried waters escape from the
> protein and whether bulk waters enter the protein.
> So, it is important for accurate placement of bulk waters before
> simulation.
> 
>>From what I can understand, genbox removes water molecules that overlap
> with protein atoms. So, for a protein with a large hydrophobic cavity,
> will added water molecules remain undeleted and expected to escape with
> time?

Yes. Experimentally (X-ray, NMR) it is known as well that interior cavities
in the protein can exchange water with bulk, and I've seen several papers
(and heard talks about) the likelihood of finding waters even inside
hydrophobic cavities - the consensus is that this chance is non-negligible!


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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