Thanks very much for the advice. I will have another look and see if I can
figure it out.
Warm regards,
Ranji
On Sun, Nov 17, 2013 at 10:35 PM, case <case.biomaps.rutgers.edu> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 18 2013 - 10:00:02 PST
