I have used vmd and pymol for the visualization of the molecule.
On 8 Dec 2017 7:57 pm, "David A Case" <david.case.rutgers.edu> wrote:
> On Fri, Dec 08, 2017, Shilpa Gupta wrote:
>
> > I have generated my initial structure which comprises of dendrimer
> solvated
> > in ionic liquid [BMIM][Cl] using packmol. The initial structure was
> > correctly bonded but after doing minimization bond between the residues
> of
> > solute are broken. I could not find any related issue in archives. What
> > could be the possible reason for this? Thanks in advance.
>
> Bonds never break during molecular mechanics simulations. How did you
> determine that bonds were present or not present? If you are using a
> visualization program, it is probably applying its own heuristics.
>
> You can use parmed to explore which bonds are present in your system.
>
> ...dac
>
>
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Received on Fri Dec 08 2017 - 08:30:02 PST
