On Mon, Sep 26, 2016, Jesmita Dhar wrote:
> I want to simulate a dipeptide sturucture
> within a system of 4.5 nm cubic water box. Please help me to solvate
> the structure in such cubic box. What will be the command?
If a box of *about* 4.5 nm in size would work, to this in tleap:
solvateBox PEP TIP3PBOX 22.0 0.8
where "PEP" is the unit name for your dipeptide. (Note that this is way more
water than you need to simulate the properties of a dipeptide in water.)
Getting a box exactly 4.5 nm on a side is actually rather difficult, since
box size changes as you run a constant pressure simulation.
...hope this helps....dac
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Received on Mon Sep 26 2016 - 05:30:03 PDT
