VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Wed Jul 07 2021 - 11:29:00 CDT

Yiyan,

VMD needs information about bonds such as a connection table or psf file. XYZ only contains coords of nuclei. Other programs will attempt to create bond order information based on distances, but will often get it wrong for a complex system that doesn't have higher-order complexity, like a complex alkane where a proton might belong to either carbon that it is near. I just randomly made a similar compound in MOE and saved it as a tripos mol2 file, and VMD was able to open that with bonds. Perhaps try a mol2 file. Also check that the drawing method you are using displays bonds. Lines for e.g. or licorice.

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Yiyan Kuang <yiyan.kuang_at_uconn.edu>
Sent: Tuesday, 6 July 2021 8:13:38 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: showing bonds in .xyz files

Hello,

I am trying to use vmd to visualize a bottle-brush polymer, I have written a .xyz file containing coordinates of monomers on both backbone and side chains like the attached document. The vmd can load and plot all the coordinates but cannot show the bonds between monomers. I was wondering if anyone has any suggestions on my issue? Thanks!

Best regards,
Yiyan