Re: [AMBER] Bonds between residues are broken

From: David A Case <>
Date: Fri, 8 Dec 2017 09:27:28 -0500

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.


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Received on Fri Dec 08 2017 - 06:30:06 PST
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