On Thu, Sep 17, 2015 at 9:48 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Jason - correct me if I'm wrong, but if you delete the bond parameter, it's
> true that it won't be there, but it won't delete the angle term between
> atoms across the previous bond, or the torsion parameters. There is also
> the problem of the nonbonded interactions. the atoms previously bonded
> won't have any nonbonded, nor will the 1-3 atoms, so these molecules can
> float on top of each other near the deleted bond. I would imagine the only
> good way to do this is to remove the bond before you make the prmtop, not
> after... unless parmed is smarter than I thought!
>
​ParmEd is smarter than you thought ;). deleteBond does all of this. It
deletes the bond in its entirety (including all other valence terms that
include that bond), and it always recomputes the exclusions before writing
a topology file.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 17 2015 - 08:30:03 PDT
