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GROMACS pdb2gmx Warning: Missing Atoms (H and O) in AlphaFold3-Derived TCR–pMHC Structure

I am using GROMACS for my TCR-pMHC structural model from AlphaFold3 and i got this warning message, should i be worried about this? I got this for each of these protein(TCR, peptide, and MHC).


(WARNING: Residue 1 named GLU of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 113 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.

md tcr-pmhc simulations gromacs

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