Dear Amber users,
since no one replied I shall rephrase my question.
My protein has two parts, covalently connected, which move 40A away from
each other during the MD. The cell dimensions were set to at least 30A
from the protein to the cell edge. Therefore, one part of my protein has
extended into the neighbouring cell. My cutoff (cut) was set to 10.
Would it be correct to assume that my results are accurate enough
because the initial distance between the protein molecules in
neighbouring cells is at least 30 x 2 = 60A, and after the protein has
moved there would still be at least 60A - 40A = 20A gap between the two
protein copies, which is more than 10A cutoff?
Thank you for your time.
P.S. Actually, I am interested only in the initial event - the two parts
of the protein separate, i.e., they do not form a stable globule. I do
not care what exactly happens afterwards.
On 07/03/2017 09:32 PM, Dmitry Suplatov wrote:
> Dear Amber users,
>
> I need to simulate a two-domain protein. The two domains are expected
> to separate during the MD. How should I select the solvation distance
> when creating a box? I.e., the box should accommodate a two-domain
> protein which becomes longer when the domains separate during the MD.
>
> My understanding is that the protein in the cell #1 must not approach
> the protein in the cell #2 closer than the specified by the 'cut'
> parameter (the close range electrostatics). Therefore, if, e.g., I
> have used the 'at least 25A' solvation distance and after the
> simulation I put the two cells together in PyMol and the two proteins
> are at least 'cut' A away from each other - than its OK. Am I right?
>
> Thanks.
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Received on Wed Jul 05 2017 - 10:30:03 PDT
