GROMACS version: 2024
GROMACS modification: Yes/No
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Hello,
I am new to Gromacs but have finished the Lysozyme tutorials. I now want to simulate 1 Na+ ion surrounded by water molecules in a cube of L = 24.83A. However, when I try to generate a topology file using any of the existing forcefields, I get the error: “Residue ’ ’ not found in residue topology database”. What would be the most appropriate forcefield to use or are there existing topology files that one can use? Thanks in advance for your help.
The forcefield already has a topology file for sodium ions (it uses this when you used genion in the ‘add ions’ step of the tutorial), but it isn’t typically included in the topologies that pdb2gmx would recognize since that command is usually for pdb files of proteins and nucleic acids.
For something like a single ion, it would be simplest to just make your own .gro and .top file. To make a .gro file for small molecules like sodium, you can search up the file containing its structure data (such as .sdf files from pubchem) and use OpenBabel to convert it to a .gro file. To make a .top file, most straightforward method would be to take an existing .top file from the tutorial and edit out everything except for a single sodium (you may need to replace CL with NA if it’s the only ion present), should look something like this (note the #include “oplsaa.ff/ions.itp” which calls the topology file from the forcefield). topol1.top (776 Bytes)
From there, just use those files as inputs as you would the files pdb2gmx generates (skipping the genion step of course)
For future reference, if you need to run a simulation of something more complex where the topology isn’t present in the forcefield, you can refer to Protein-Ligand Complex