# Error with pdb2gmx when peptide is capped
**URL:** https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047
**Category:** User discussions
**Created:** [November 4, 2020, 4:24pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047 "2020-11-04T16:24:17Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@js10230](https://gromacs.bioexcel.eu/u/js10230)
#### Post date: [November 4, 2020, 4:24pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047/1 "2020-11-04T16:24:17Z")
GROMACS version: 2018.3
GROMACS modification: No
I created a peptide (7-residue long) and capped it such that **ACE-(peptide)-NME**.
When I ran the pdb2gmx (_gmx pdb2gmx -f peptide.pdb -o peptide.gro -ignh -ter_), I got an error saying, _Atom X in residue YYY not found in rtp entry_, so I fixed the problem by changing the atom’s name to whatever is compatible with the force field (CHARMM36-m).
But this time I get another error: _Residue 9 named NME of a molecule in the input file was mapped to an entry in the topology database, but the atom CH3 used in that entry is not found in the input file…_
I do have the CH3 in my PDB file. Can anyone help me with this problem? Thanks.
---
### Author:  [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)
#### Post date: [November 5, 2020, 9:20am UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047/2 "2020-11-05T09:20:06Z")
Hi,
As far as I understood you have defined the termini in your peptide with a specific entry in the rtp file (e.i NME). In this case you do not need the option -ter. Did you try to run without the option -ter ?
Best regards
Alessandra
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [November 5, 2020, 2:24pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047/3 "2020-11-05T14:24:00Z")
The NME residue definition in the CHARMM36 port for GROMACS is not fully consistent with an input coordinate file generated by CHARMM, which will have CAT instead of CH3. I will rectify this in a future version of the port but for now the solution is to change the atom name(s) in the input coordinates to match the `.rtp` entry for NME.
---
### Author:  [@js10230](https://gromacs.bioexcel.eu/u/js10230)
#### Post date: [November 5, 2020, 3:54pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047/4 "2020-11-05T15:54:50Z")
Hi,
Thank you for the reply. When I didn’t include the option “-ter”, I got _Atom N in residue 1ACE not found in rtp entry_. pdb2gmx automatically tried to look for or add NH3+ to the ACE and COO- to the NME.
But first of all my ACE is 0ACE, not 1ACE. Secondly, the ACE doesn’t have any N atoms.
---
### Author:  [@js10230](https://gromacs.bioexcel.eu/u/js10230)
#### Post date: [November 5, 2020, 3:57pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047/5 "2020-11-05T15:57:40Z")
Thank you for the reply.
I think it’s working now. I changed all the names of the atoms of my NME to match those in the .rtp entry, and I am now at the MD production step without any errors.
And it seems the “-ter” option is necessary in the pdb2gmx, especially when I am dealing with a capped peptide.
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [November 5, 2020, 4:54pm UTC](https://gromacs.bioexcel.eu/t/error-with-pdb2gmx-when-peptide-is-capped/1047/6 "2020-11-05T16:54:56Z")
The CHARMM36 force field always requires the explicit use of `-ter` since there are not separate `.rtp` files for protein and nucleic acid residues. This is a consequence of how we have to do the file conversion.