[gmx-users] Broken bonds between peptide and capped terminals when solvated

Dallas Warren dallas.warren at monash.edu
Tue May 28 00:04:10 CEST 2019

VMD has no knowledge of bonds, as all you fed it was a coordinate
file. It makes guesses based on the separation of the atoms which
atoms are bonded or not. So no bonds are being broken.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 27 May 2019 at 15:12, Dilip.H.N <cy16f01.dilip at nitk.edu.in> wrote:
> Hi all,
> I have a capped peptide and when i solvate the system with water and
> visualize it in vmd, the bonds between the peptide and corresponding capped
> N and C terminal groups is not seen (or) broken.
> Whereas before solvating the system, the bonds between the peptide and
> corresponding capped N and C terminals are intact when visualized in vmd.
> Why is this happening? After solvating the peptide system, why are the
> bonds between peptide and capped terminal groups getting broken.?
> How can i solve this issue...?
> Any suggestions are highly appreciated.
> Thank you.
> ---
> With Best Regards,
> Dilip.H.N
> Ph.D. Student.
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