# Error in pdb2gmx while parsing cyclic peptide

**URL:** <https://gromacs.bioexcel.eu/t/error-in-pdb2gmx-while-parsing-cyclic-peptide/10600>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [November 21, 2024, 6:52am UTC](https://gromacs.bioexcel.eu/t/error-in-pdb2gmx-while-parsing-cyclic-peptide/10600 "2024-11-21T06:52:08Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![sushil-sys](https://avatars.discourse-cdn.com/v4/letter/s/43a26b/32.png) [@sushil-sys](https://gromacs.bioexcel.eu/u/sushil-sys)\
**Post date:** [November 21, 2024, 6:52am UTC](https://gromacs.bioexcel.eu/t/error-in-pdb2gmx-while-parsing-cyclic-peptide/10600/1 "2024-11-21T06:52:08Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
I am getting an error “Atom O in residue KYT 14 was not found in rtp entry KYT with 31 atoms  
while sorting atoms.”

The KYT residue is a custom residue. This is the last residue which connects to sidechain of one of the initial residue through  
ester bond by using C-terminal. The KYT residue is parameterized to include the sidechain of the intital residue which connects to the C-terminal.

In order to include the Custom residues and the the ester bond connection the aminoacids.rtp file and aminoacids.hdb has been modified to include them.

Yet I am receiving this error. I presume by this error the pdb2gmx is trying to look for C-terminal O which of course would not be present.

I am using charmm36m forcefield to model the molecule. It is similar to surfactin.

Can you please guide as to how to approach the issue. The peptide has a cyclic part in it.