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Here post your question I am facing difficulties while generating the topology file. Specifically, I am trying to simulate molecules like naphthalene or anthracene to study the interaction with water molecule, but I keep encountering an error during the generation of the topology file. While giving the force field and water model to the naphthalene pdb file that I have generated, it is showing the error as residue ligand not found in the residue topology database. Can anyone explain this issue and give me a solution?I even tried to edit the pdb file but still facing the issue.
Hi,
Please specify which tool give you the error.
Usually in the topology generation phase, the rtp (residue topology database) File formats - GROMACS 2024.5 documentation
should contain all the entries/names present the pdb file to allow the tool (e.i gmx pdb2gmx) to build a topology file for the specific system.
In your case, my guess is that the ligand is not properly defined in the rtp file
\Alessandra
Thank you for your reply, ma’am.
And Yes, I am aware that not all ligands are included in the gmx pdb2gmx tool. However, I only have the PDB file at the moment. I converted the naphthalene PDB file to mol2 format for generating the ITP file using SwissParam, but I’m still encountering an error.
If I had the ITP file, I would manually write the topology file for both the naphthalene and water molecules. Could you kindly explain where I can obtain the source ITP files for these molecules?
(P.S. I also tried modifying the entries in the PDB file to allow gmx pdb2gmx to generate the topology, but the error persists.)