From: Vermaas, Joshua (
Date: Wed Nov 21 2018 - 11:43:43 CST

The addbond may also need the angles and dihedrals to be guessed again, depending on the force field you are using.


On 2018-11-21 00:18:12-07:00 wrote:

On Wed, Nov 21, 2018 at 11:44 AM Monika Madhavi <<>> wrote:
Dear all,
I have a pdb of a parallelepiped unit cell of a solid. I want to create a slab of this solid by repeating the unit cell along x,y and z directions.
See replicatemol command from topotools. Link:>
If your aim is to "create a slab of this solid by repeating", then you might want to use "addbond" command to covalently bond between atoms at the interface of cells.
I can add images of the unit cell in the x,y and z directions by using the "Graphics -> Representations -> Periodic" in vmd and by enabling periodic images to draw. Is there any method to save the visualization as a pdb? or what is the easiest method to create such a pdb from the pdb of the unit cell I have?
Thank you.
Best regards,

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.
Devanand T
SRF (Computational Biology) @ IMSc, Chennai
Phone (off) : 91-44-22543108
Mobile : 91-9791479561
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