Thanks Jason and Bill,
I'd like to know if I just need to calculate the free energy (actually
without entropy) of my ligand, do I just have to ignore the receptor_mask
in my input file?
Yi
On Fri, Jul 19, 2013 at 4:46 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Jul 19, 2013, at 3:03 PM, Bill Miller III <brmilleriii.gmail.com>
> wrote:
>
> > No, the python version also supports the triple trajectory protocol.
>
> And in fact supports the even more seldomly used double trajectory
> protocol. The AmberTools manual has a chapter on MMPBSA.py that should have
> explicit instructions on running a multiple trajectory binding free energy
> calculation.
>
> In fact, MMPBSA.py also supports molsurf SA calcs now, too, so MMPBSA.py
> should implement just about all of the mm_pbsa.pl functionality.
>
> HTH,
> Jason
>
> _______________________________________________
> 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 Fri Jul 19 2013 - 16:00:02 PDT
