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
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Received on Thu Jun 12 2014 - 04:30:02 PDT
