GROMACS version: 2020.1
I want to run a host-ligand simulation with CHARMM36 FF. The parameters of the ligand (PRG) were obtained before and stored as CHARMM .prm file. Then, I used TopoTools in VMD (with the
writegmxtop function) to obtain the ligand’s parameters/topology as an .itp file. With this I want to build the topology for the complex. When I run pdb2gmx (
gmx pdb2gmx -f complex.pdb -o complex.gro -p complex_topol.top -i PRG.itp -water tip3p) I get:
Fatal error: Residue 'PRG' not found in residue topology database
Is there any way to override the inclusion of the new residue in the .rtp file and just
#include it in the topology?
Thanks in advance.