Adding a new residue to topology

User discussions
1

GROMACS version: 2020.1
GROMACS modification:

Hello,

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.

Best regards

2

See Protein-Ligand Complex

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