Fatal error: Atom HO2' in residue A 21 was not found in rtp entry ADE with 31 atoms while sorting

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1

Hi,

I have a .pdb file of a single-stranded RNA 20mer. I am using the charmm36 forcefield from July 2022.

I want to use pdb2gmx to generate topology files.

Inspired by a prior post which had my initial error, I tried choosing 5TER and 3TER for the terminus types, but I am getting a fatal error.

gmx pdb2gmx -f mrna.pdb -o mrna.gro -ter

I select 5TER for A start terminus and 3TER for U end terminus.

I get this error:

Fatal error:
Atom HO2' in residue A 21 was not found in rtp entry ADE with 31 atoms
while sorting atoms.

How can I solve this? For reference, below are screenshots of the A starting nucleotide and U ending nucleotide.

image
image826×917 144 KB

image
image826×917 158 KB

I also tried using -ignh, but then this results in the error:

Fatal error:
Atom OP1 in residue U 2 was not found in rtp entry URA with 30 atoms
while sorting atoms.

Thanks for the help!

2

Simply put, the atom names do not comply with what the force field expects. Hydrogen naming is easily fixed with the -ignh option. If you want to preserve the hydrogen coordinates, you have to rename them yourself (HO2’ should be H2’’ for CHARMM). Similarly OP1 → O1P and OP2 → O2P.