I've a new ligand and named it as 'UNK' in pdb file. While generating the ligand topology through GROMACS by following its protein-ligand tutorial. I'm getting this fatal error: " Residue 'UNK' not found in residue topology database.". What does it mean and how do I rectify it?
Check your mol2/itp file of ligand there would be the exact thing. whether UNK or LIG or anything. Use that in topol.top.
HTH!
Hi Bhavya,
It seems that you are not adding the force field of your ligand (drg.itp) properly in your topol file. top. The other reason could be that you are not adding the file generated in PRODRG (file.gro) correctly to form the protein-binding complex.
pdb2gmx can only write topologies for molecules that it knows. Generally, you cannot process ligands or non-biomolecular species with pdb2gmx. See an example approach at http://www.mdtutorials.com/gmx/complex/index.html
Check your mol2/itp file of ligand there would be the exact thing. whether UNK or LIG or anything. Use that in topol.top.
HTH!
So everyone is clear - this is a specific error message that comes from pdb2gmx that has a well established explanation and solution: http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database It has nothing to do with mol2 files or adjustments to topologies. The problem is that the topology cannot be created because an .rtp entry does not exist for the ligand, generically named UNK.
@Justin Lemkul, sir i encounted similar problem in AMBER MD and was resolved this way!
Justin Lemkul , Thank you for answering. I followed the same procedure, by trying to generate ligand topology through CGENFF. But charge penalty was 54. How do I rectify it?
Martiniano Bello & Anwesh Pandey , Thank you for answering. I tried to generate the ligand topology through GROMACS without using any external tools.
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