# Error in pdb2gmx

**URL:** https://gromacs.bioexcel.eu/t/error-in-pdb2gmx/3944
**Category:** User discussions
**Tags:** forcefield, pdb2gmx, mdrun, simulation-setup
**Created:** [April 2, 2022, 2:30am UTC](https://gromacs.bioexcel.eu/t/error-in-pdb2gmx/3944 "2022-04-02T02:30:46Z")
**Posts on this page:** 3
**Page:** 1

<div class="post-metadata">

### Author: ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)
#### Post date: [April 2, 2022, 2:30am UTC](https://gromacs.bioexcel.eu/t/error-in-pdb2gmx/3944/1 "2022-04-02T02:30:46Z")

</div>

GROMACS version:2020  
GROMACS modification: Yes/No  
Here post your question  
Dear Researcher,  
I have faced a problem in converting pdb2gmx. In that stage, I faced hydrogen atom error. So used -ignh flag. It is good to ignore hydrogen atoms during the conversion of pdb2gmx. or Should I renamed it according to rtp files

Your help i highly appreciated

---

<div class="post-metadata">

### Author: ![gvigers](https://avatars.discourse-cdn.com/v4/letter/g/a9a28c/32.png) [@gvigers](https://gromacs.bioexcel.eu/u/gvigers)
#### Post date: [April 7, 2022, 12:27pm UTC](https://gromacs.bioexcel.eu/t/error-in-pdb2gmx/3944/2 "2022-04-07T12:27:05Z")

</div>

Yes. “-ignh” will ignore the hydrogens in the input file and will then add back the hydrogens required to complete the structure. I have never seen a problem with this process - pdb2gmx does an excellent job.

---

<div class="post-metadata">

### Author: ![Santosh456](https://avatars.discourse-cdn.com/v4/letter/s/a8b319/32.png) [@Santosh456](https://gromacs.bioexcel.eu/u/Santosh456)
#### Post date: [April 7, 2022, 5:12pm UTC](https://gromacs.bioexcel.eu/t/error-in-pdb2gmx/3944/3 "2022-04-07T17:12:32Z")

</div>

Thank You