I am performing simulation on gromacs and in protein topology step fatal error came which says “Atom HB3 in residue ASN 34 was not found in rtp entry ASN with 16 atoms while sorting atoms”
Kindly help me in fixing this error
The forcefield you’re using has a list of atoms and their parameters which it expects for the residue ASN, this error means the file you’re storing the protein information in lists an atom not under the residue entry. If you look in the folder containing the forcefield you’re using, you should be able to find a file listing out the atoms and parameters for the amino acid residues, the atoms for ASN should match those which the forcefield has listed under ASN to work.
If your simulation requires the parameters to be different for whatever reason, you should be able to either edit the forcefield you’re using (see KALP-15 in DPPC for an example of how this is done with lipid parameters) or define your own .itp file and reference them in the topology file (see Protein-Ligand Complex for how to define the parameters for a ligand)
Use pdb2gmx -ignh and have it rebuild H atoms. This is frequently encountered in PDB files that use e.g. HB2 and HB3 instead of what GROMACS expects (HB1 and HB2).