I am running the cg_bonds.tcl script with the command:
cg_bonds -top ramp_GIISK_50pep.top -topoltype "elastic"
My system consists of proteins, CA ions, CL ions, W molecules and DPPC and RAMP (RaLPS). I get the error: one atom appears twice in list cg_bonds.tcl on VMD
Can anyone help me?
It has worked before with my other protein-lipid systems!