From: Vermaas, Joshua (
Date: Tue Nov 12 2019 - 18:01:55 CST


One thing to try would be to see if using VMD 1.9.3 fixes the problem. I can't recall if this script cared about the VMD version or not. There are two other things you can try too:

Is there anything funky in your structure that might cause the cg_bonds script trouble? I recall using it before, but also remember getting frustrated with its performance, and that was what lead me to make my own tpr reader.


On 2019-11-12 16:00:33-07:00 wrote:

Dear VMD users,
I did md simulation of amphiphile peptides using gromacs and Martini force field.
I loaded trajectory file in VMD. Then, I used following commands in TkConsole:
1) source cg_bonds.tcl
2) cg_bonds -tpr new.tpr -top -topoltype "elastic"
I encountered with:
atomsel : setbonds: Need one bondlist for each selected atom
version of gromacs is 2018.8
version of VMD is 1.9.1
I used cg_bonds.tcl script from this web site:
How to resolve this problem?