Re: [AMBER] making a box with restraints so ligand does not float away

From: case <>
Date: Sun, 17 Nov 2013 17:35:14 -0500

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:
> 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

AMBER mailing list
Received on Sun Nov 17 2013 - 15:00:02 PST
Custom Search