VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Tue Sep 17 2024 - 01:49:40 CDT

Long back, I used to get this error. I remember doing two things then: copy cg_bonds.tcl in the directory where .top file is located and then source it. Second, I modified the gmx path to my Gromacs installation.

There might have been other modifications that I did but I remember atleast these two. If this doesn't help, let me know.

Regards,
Raman

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________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Samapika Sahu (P20CY011) <sahu.14_at_iitj.ac.in>
Sent: Tuesday, September 17, 2024 12:19:31 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Visualizing elastic network proteins

Dear developers

I am working with a coarse-grained MARTINI system. My system contains a beta-sheet protein, which is modeled using an elastic network, and the bilayer contains MARTINI-3 lipids. I am trying to visualize the protein without an elastic network, for which I am giving the following commands in the TK console:
vmd > source /home/user/scripts/cg_bonds.tcl
vmd > cg_bonds -top vmd.top -topoltype "elastic"

But the error that crops up is: atomsel : setbonds: Need one bondlist for each selected atom
Tried searching a lot in the web but did not get a clue.
How do I solve this? Any help in this regard would be really helpful.

Thanks and Regards
Samapika