Thank you Jason. I ll update you with the results.
On Thu, Jun 12, 2014 at 7:11 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Jun 12, 2014 at 3:28 AM, maryam azimzadehirani <
> maryamai1988.gmail.com> wrote:
>
> > Dear Amber users,
> > I am calculation binding energy using MMPBSA.py on AMBER 12, I tried
> three
> > times and chose different number of frames of my trajectory. In the
> output
> > file I always get huge values for my VDW contribution. In my system I
> have
> > some attached glycans near to the binding site, but not directly in the
> > bonding site, I am taking them into calculations as well, but I don’t
> think
> > that may be the reason for huge VDW values since I have the similar out
> > values even in the absence of sugars.
> > I copied the out put file here. Will be very grateful if you guide me
> with
> > the possible solutions,
> >
>
> The only way vdW energies can be high is if two atoms get close to one
> another. This does not necessarily indicate a problem, as other terms can
> compensate. Try visualizing the system and see if anything looks strange
> (check the trajectories generated by MMPBSA.py).
>
> The checkoverlaps command in cpptraj can help locate close contacts if
> they exist.
>
> The major problem I see is the nonpolar solvation term computed in the PB
> part. I suggest using inp=1 instead of inp=2 (the default).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 Jun 12 2014 - 05:00:02 PDT
