VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
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.

-Josh

On 2018-11-21 00:18:12-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:

On Wed, Nov 21, 2018 at 11:44 AM Monika Madhavi <monikamadhavi_at_gmail.com<mailto:monikamadhavi_at_gmail.com>> 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: https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/#TOC-replicatemol-mol-nx-ny-nz-a.Vermaas%40nrel.gov%7C861a4af205824aac41f208d64f817d9d%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636783814917473753&sdata=SXwoPOTl89%2F9qp2jF416pGN%2FDvh7jYeV40lxQDzfL3U%3D&reserved=0>
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,
Monika 

--
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.
--
regards,
Devanand T
SRF (Computational Biology) @ IMSc, Chennai
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