On Sun, Nov 17, 2013, ranjit pillai wrote:
>
> I am trying to make a box around a protein and ligand in explicit solvent,
> so that binding events can be captured as shown in this paper:
>
> http://www.pnas.org/content/early/2011/05/31/1103547108
>
> The paper uses flat bottomed harmonic restraints to make the box and
> prevent the ligand from floating away from the protein. I read advanced
> tutorial 4 on distance restraints, but don't think this is going to help
> make the box.
>
> I'm a bit overwhelmed by the restraint section in the manual and was hoping
> someone knew a good method for creating the box that could be used with the
> GPU code in amber 12?
Almost all explicit solvent simulations use a periodic box; it is typically
set up when you use the solvateBox or solvateOct command in LEaP. Concentrate
on section 6.1 to learn about artificial constraints.
Note that you had better plan to gain a lot experience with simpler systems
first if you plan anything like the calculations reported in the paper you
cite (which generated 50 microseconds of simulation).
...good luck...dac
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Received on Sun Nov 17 2013 - 15:00:02 PST
