also make sure you are using Amber11 or later.
On Mon, Apr 18, 2011 at 11:51 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mahmoud,
>
> > I wonder can I do NEB calculations to find the lowest energy path
> > between
> > two points (Reactant and product) for a reaction happens between a
> > ligand
> > and enzyme using QM/MM approach? or that would be difficult due the
> > fact
> > that in enzymes there will be thousands of degrees of freedom. If my
> > guess
> > is true, is there any alternative to do a simple QM/MM potential
> > energy
> > surface? any tutorial on that?
>
> You can certainly do it the code will allow it. How well it will work will
> very much depend on how you setup the calculation, the QM region you choose
> and whether the QM theory model you use is appropriate for that reaction.
> As
> long as the bond is broken within the QM region though there is nothing
> stopping you running this. You will just have to be careful building your
> two end point prmtops. I suggest checking the literature for everything
> involving NEB before you start though.
>
> Good luck,
>
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
> _______________________________________________
> 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 Apr 18 2011 - 09:00:10 PDT
