Unknown bond_atomtype CG2DC2

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes/No
Hi there, I am trying to run MD simulation with one of the molecules that I just parametarized by using CGENFF force field. The penalty is low (2.3) and it seems that parametarization was correct. When trying to run energy minimization with the whole system that contains molecule, I get the error “Unknown bond_atomtype CG2DC2”. I have tried to use different releases of charm36 forcefield, but same error keeps occuring. Anyone knows how to solve this issue?

This is my top file:
;; Generated by CHARMM-GUI FF-Converter
;;
;; Correspondance:
;;
;; The main GROMACS topology file
;;

; Include forcefield parameters
;#include “/hosts/me/charmm36_CHARMMGUI_CGenFF/forcefield.itp”

#include “…/toppar/sob.prm”
#include “…/toppar/DPPGK.prm”
#include “…/toppar/POPG.itp”
#include “…/toppar/DPPGK.itp”
#include “…/toppar/PVCL2.itp”
#include “…/toppar/POT.itp”
#include “…/toppar/CLA.itp”
#include “…/toppar/TIP3.itp”
#include “…/toppar/TIPX.itp”
#include “…/toppar/sob.itp”

[ system ]
; Name
Title

[ molecules ]
; Compound #mols
POPG 114
DPPGK 76
PVCL2 10
POT 78
CLA 20
TIP3 7222
TIPX 1137
sob 14

2

Did you generate the whole system with CHARMM-GUI, or did you have an existing system to which you added a ligand that you parametrized separately? Note that CHARMM-GUI is rather inflexible in this regard as it only provides you with the subset of the CHARMM force field that applies to your system. So if you add something else to it later, it may not have all the parameters you need.