GROMACS version: 2024.4
GROMACS modification: Yes/No
Hi,
I am trying to include a ligand (calcein) parameterized using CGenFF with CHARMM36 (July 2022) force field in GROMACS.
However, I am getting multiple errors like:
ERROR: No default Bond types
ERROR: No default U-B types
ERROR: No default Proper Dih. types
What I have done:
- Generated calcein.itp from CGenFF
- Included it in topol.top
- Used charmm36_ljpme-jul2022.ff for generating calcein.itp file.
My topol.top (relevant part):
topol.top (899 Bytes)
calc.txt (29.7 KB)
Could you please suggest what I might be missing?
Your suggestions will be highly appreciated.
Thanks & Regards
Kankana Bhattacharjee
Use the latest version of the C36 port for GROMACS; we updated it last month. The server is using a much newer version of the force field, which assumes that certain parameters are in the core parameter set. Those will be missing from your topology because your molecule’s topology relies on them being present in the core set, which they aren’t in the 2022 version.
Ok. Thank you for the clarification.
That means, have to add latest charmm36-2024.ff in GMXLIB, so that CGenFF parameters become compatible ?
As with any force field, either in $GMXLIB or the working directory.
Dear Sir,
I have downloaded the latest C36 port for gromacs and included that in the topol.top file, but still getting the same error.
; Include force field files
#include “charmm36-feb2026_ljpme_cgenff-4.6.ff/forcefield.itp”
; Include lipid topology
#include “DMPC.itp”
; Include ligand topology
#include “calc.itp”
; Include water model and ions
#include “charmm36-feb2026_ljpme_cgenff-4.6.ff/tip3p.itp”
#include “charmm36-feb2026_ljpme_cgenff-4.6.ff/ions.itp”
[ system ]
DMPC-calcein-solvated system
[ molecules ]
; molecule name number
DMPC 128 ; number of lipid molecules in bilayer
CALC 1 ; number of calcein molecules
SOL 16298
Thanks & Regards
Kankana Bhattacharjee