Fatal error: Residue 180 named LEU , Post PRA server Atom HE2 in residue HIS 891 was not found

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
Fatal error:
Residue 180 named LEU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

Used protein-science.comrotonation/ default settings to resolve above error but got another error with pdf file, mentioned below:

Fatal error:
Atom HE2 in residue HIS 891 was not found in rtp entry HID with 17 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.

Can you suggest correct way to resolve this, as i am new in MD simulation.
Thanks

2

If you don’t need to care about histidine protonation states, adding -ignh to gmx pdb2gmx should fix it (all hydrogens will be rebuilt from scratch). If you want to specify HIS states one by one, use -his additionally to toggle on interactive selection.

4

Thanks for the reply but no use its through another error:

Fatal error:
Atom OXT in residue LYS 965 was not found in rtp entry LYS with 22 atoms
while sorting atoms.

5

You should let gmx pdb2gmx know it’s a terminal residue. Add chain information, or include a TER line at the end, and see if that helps.

Essentially, the OXT atom marks the C-terminus in a PDB, but unless there are other hints for the program to identify the C-terminal residue of a chain, it won’t know to apply the terminal patches or use alternative residue definitions.

6

Thanks, but TER at the end didn’t work and through the same error, which is "Fatal error:
Residue 180 named LEU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

7

pdb2gmx expects to find an atom named CG in the input coordinate file, and it’s telling you it doesn’t. Either it has an incorrect name (as some programs often do not adhere to IUPAC/IUPAB standards) or it’s simply not there (missing entirely because it isn’t resolved in the structure). You need to investigate which case applies and take suitable action, either by renaming the atom (simple) or reconstructing the residue (not too hard, but not something you can do in GROMACS).

8

Thanks a lot man your simple explanation helped me to find the actual issue , its 580 resiude which is missing CG, CD1 and CD2 . unfortunately reconstructing is not easy for me, can you suggest how i can add CG, CD1 and CD2 in my protein at 580 position. it will be a great help.

9

There are lots of different modeling programs that can build in missing residues or sidechains. Pass it through any of those and you should have a usable coordinate file.

10

Thanks , i remodelled my protein and it got resolved. :)