Fatal error: Atom OXT in residue VAL 10 was not found in rtp entry VAL with 16 atoms while sorting

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GROMACS version: 2024.2
GROMACS modification: Yes/No
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I have been trying to get the topology file for a peptide by using pdb2gmx
Command used: gmx pdb2gmx -f pep.pdb -o pep.gro -p topol.top -ignh

I have also checked the aminoacid.rtp file. There is not OXT in that file
How can i fix this issue ?

2

Is this peptide made from the standard amino acids? If so, there might be some difference in naming convention you need to fix in the .pdb file. Try checking what atoms are supposed to be in VAL based on aminoacid.rtp and see if the issue is some atoms need to be renamed in the pdb. You could also check the residues adjacent to the VAL residue to see if the error is from those other residues.

If the peptide isn’t supposed to be one of the standard amino acids, you may need to generate your own topology for it (this tutorial should be a good reference)