# Problem with acetylated and amidated termini in pdb2gmx command

**URL:** <https://gromacs.bioexcel.eu/t/problem-with-acetylated-and-amidated-termini-in-pdb2gmx-command/3200>\
**Category:** User discussions\
**Tags:** pdb2gmx, forcefield\
**Created:** [November 24, 2021, 9:23pm UTC](https://gromacs.bioexcel.eu/t/problem-with-acetylated-and-amidated-termini-in-pdb2gmx-command/3200 "2021-11-24T21:23:50Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![awfully\_silent](https://avatars.discourse-cdn.com/v4/letter/a/b2d939/32.png) [@awfully\_silent](https://gromacs.bioexcel.eu/u/awfully_silent)\
**Post date:** [November 24, 2021, 9:23pm UTC](https://gromacs.bioexcel.eu/t/problem-with-acetylated-and-amidated-termini-in-pdb2gmx-command/3200/1 "2021-11-24T21:23:50Z")

</div>

GROMACS version: 2018.6  
GROMACS modification: No

I was trying to generate .gro file from a pdb file using pdb2gmx with CHARMM22\* force field. The N terminal of my peptide is acetylated Asn and the C terminal is amidated Ala. When I ran the pdb2gmx command with -ignh and -ter, I chose “None” when being prompted to select termini types, and I got the error:

Fatal error:  
There is a dangling bond at at least one of the terminal ends. Fix your  
coordinate file, add a new terminal database entry (.tdb), or select the  
proper existing terminal entry.

Is there anything I can do to fix it? Thank you!!

---

<div class="post-metadata">

**Author:** ![yenn](https://avatars.discourse-cdn.com/v4/letter/y/c37758/32.png) [@yenn](https://gromacs.bioexcel.eu/u/yenn)\
**Post date:** [March 6, 2024, 12:21am UTC](https://gromacs.bioexcel.eu/t/problem-with-acetylated-and-amidated-termini-in-pdb2gmx-command/3200/2 "2024-03-06T00:21:31Z")

</div>

Hi, I have the same problem… Did you fix it?