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

[Dilip.H.N]

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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27/05/19,
10:33:05