GROMACS version:2022.2
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After performing protein-protein molecular docking, I want to try molecular dynamics simulations. To make it easier to distinguish, I changed one protein to chain A and the other protein to chain B. The input command is: gmx pdb2gmx -f protein.pdb -o protein_processed.gro -ignh -ter.
After running the command, the following error appears: Fatal error: Atom OXT in residue GLN 336 was not found in rtp entry GLN with 17 atoms while sorting atoms.
Does this error mean that I need to delete the OXT atom in GLN 336? If I delete it, will it significantly affect the results of the molecular dynamics simulation?
OXT is a C-terminal carboxylate oxygen, indicating the end of a chain. What you have labeled as chain B is therefore discontinuous, with either missing residues between 336 and 343, or whatever alteration you made in renaming the chains was incorrectly done. If Leu343 is supposed to start a new chain and Gln336 is actually a terminus, you need to use a distinct chain identifier starting with Leu343 or insert a TER card between them.
Hello, this is the receptor PDB file downloaded from HDOCK after docking two proteins. I want to perform molecular dynamics simulations, but both the ligand PDB and receptor PDB only have one chain. The receptor PDB and ligand PDB both have chain A. To make it easier to differentiate, I renamed the ligand PDB to chain A, and changed the receptor PDB to chain B. After docking, the receptor PDB file contains an OXT atom at residue 336. Do you mean that after docking, the receptor PDB was split from one chain into two chains? Should I insert a TER card after residue 336, or should I delete the OXT atom line at 336? receptor .txt (523.8 KB)
You have a discontinuity in chain B. If that’s what came out of HDOCK, probably it is using an artificial (incorrect) terminus for Gln336 and the residues from 337-342 need to be modeled in.
