VMD-L Mailing List

From: leila karami (karami.leila1_at_gmail.com)
Date: Tue Nov 12 2019 - 15:18:08 CST

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 C16.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:
http://md.chem.rug.nl/images/tools/VMD/cg_bonds.tcl

How to resolve this problem?

Best,
LK