Does minimization use PME?
Bill
> Take a look at the imin=3D5 option in sander (manual). That will let
> you process a trajectory just as though it were a series of input
> coordinate files. Choosing a maxcyc of 0 or 1 will simply extract the
> energies. I believe you are able to set ntb=3D1 or 2 (equivalent in the
> case of a single-point energy calculation I believe). You can then
> proceed to use ptraj to strip the ligand from the receptor and analyze
> the receptor alone with this method and the same for the ligand
> (you'll need separate, compatible prmtops for each step). Then taking
> the difference complex - receptor - ligand will give you the binding
> energy. This is basically MM/PBSA with periodic boundary
> conditions...
>
> Good luck!
> Jason
>
> On Thu, Apr 15, 2010 at 1:11 AM, juan zeng <azengjuan.gmail.com> wrote:
> > Dear amber users:
> > =A0 =A0 =A0 =A0 =A0I want to calculate the binding affinity on protein-li=
> gand complex
> > with the linear interaction energy method,in this environment the binding
> > affinity comprises Van der waals interaction potential and electrocstatic
> > interaction potential.while others used the non-periodic boundary conditi=
> on
> > to calculate the binding affinity before,now I wish that this calculation
> > can be done in the periodic boundary condition.but the molecules in cell =
> far
> > away from the center cell will interaction with the protein-ligand comple=
> x
> > in the center cell,so I need to find out a method that can calculate the
> > interaction energy(especially the electrostatic interaction energy) of th=
> e
> > complex with all other molecules in the whole simulation system.Can you g=
> ive
> > me some suggestion how to make this calculation be realized.
> > =A0 =A0 =A0 =A0Hope receive your reply.
> >
> > Juanzeng
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --=20
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
> 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 Thu Apr 15 2010 - 08:30:02 PDT
