On Mon, Apr 4, 2016 at 5:42 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
> Dear All,
>
> I have a system with two carbohydrate molecules, each consists of four
> residues. I basically want to turn off all the non bonded interactions
> between these two molecules. For that, I use parmed with the following
> command (after loading the original prmtop file)
>
> addExclusions :1-4 :5-8
> outparm new.prmtop
>
This is somewhat risky. In sander and pmemd, this *only* works when using
the GB code path to calculate electrostatics. Which means it can't be used
with PME or periodic boundary conditions in sander or pmemd. To do a gas
phase calculation (i.e., with no GB model), set igb=6 in the &cntrl
namelist. Then you should see a difference.
This happens because sander and pmemd "recompute" the nonbonded exception
parameters from the list of bonds, angles, and torsions rather than using
the one stored in the prmtop file. I had written the "addExclusions"
action before I figured this out.
If you need these exclusions in a PME calculation, you'll need to use
another program that *does* respect these additional exclusion rules. For
example, OpenMM (which you can access via the "OpenMM" command in ParmEd to
run a sander-like simulation).
HTH,
Jason
--
Jason M. Swails
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Received on Mon Apr 04 2016 - 09:30:04 PDT
