Dear Gromacs users
I want to do MD simulation for my protein but when I run pdb2gmx command I am facing this error:-
WARNING: WARNING: Residue 197 named PRO 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 dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
WARNING: WARNING: Residue 463 named PRO 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 dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
I also tried with -ignh flag but still warning is the same.
I have looked for crystal structure file for missing residues and there are not missing residues related to the residues above, also the PRO amino acids it is asking about are not existing in my protein I have different residues at 197 and 463 positions.
At 197 position I have TYR and ARG at position 463.
Could you please suggest me how to resolve this issue and why it is giving a residue number or name wrong?
Thank you in advance.
Sadaf
Hi Sadaf Rani ,
I faced the same issue as well. This usually means that an atom is missing in one of the Proline residues, and it is possible that the proline residue is not connected with the rest of the protein at all. I suggest you visualise all Proline residues in your protein and figure out its residue ID. You can fix this by deleting the proline residue and re-modelling it using Modeller or similar software.
If you already have figured how to solve it in another way, I'd love to know.
Dheeraj Prakaash thank you for your kind reply. I had a missing terminal atom at the end of the chain which was causing this problem on carefully inspecting the original PDB file and comparing with mine I solved this.
Thanks.
Hey, what would you do if the original PDB itself has a missing terminal atom? I am facing this same issue - Fatal error:
Residue 1 named THR of a molecule in the input file was mapped
to an entry in the topology database, but the atom OG1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
But my Original PDB 1p44 does not contain any THR1 residue.
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