# Atomname problem while adding a residue to a forcefield

**URL:** <https://gromacs.bioexcel.eu/t/atomname-problem-while-adding-a-residue-to-a-forcefield/2012>\
**Category:** User discussions\
**Tags:** pdb2gmx, forcefield\
**Created:** [April 22, 2021, 12:11pm UTC](https://gromacs.bioexcel.eu/t/atomname-problem-while-adding-a-residue-to-a-forcefield/2012 "2021-04-22T12:11:34Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![s\_llabres](https://avatars.discourse-cdn.com/v4/letter/s/c2a13f/32.png) [@s\_llabres](https://gromacs.bioexcel.eu/u/s_llabres)\
**Post date:** [April 22, 2021, 12:11pm UTC](https://gromacs.bioexcel.eu/t/atomname-problem-while-adding-a-residue-to-a-forcefield/2012/1 "2021-04-22T12:11:34Z")

</div>

GROMACS version: 2018  
GROMACS modification: Yes/No

Dear Gromacs community,

I am trying to add a modified Histidine residue to the AMBER14SB forcefield. I have followed the instructions in the GROMACS webpage to do so ([http://www.gromacs.org/Documentation\_of\_outdated\_versions/How-tos/Adding\_a\_Residue\_to\_a\_Force\_Field](http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Adding_a_Residue_to_a_Force_Field)) and I found a problem I am struggling to understand:

I try to use pdb2gmx with the modified forcefield and it returns the following error:

> Fatal error:  
> Atom HAA11 not found in rtp database in residue HIH, it looks a bit like HAA1  
> For more information and tips for troubleshooting, please check the GROMACS  
> website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)

The problematic atom is named HAA1 and I cannot understand why pdb2gmx reads HAA11. You can see here that there is no atom HAA11 in the forcefield:

> grep “HAA1” amber14sb\_parmbsc1\_modHIH.ff/\*  
> amber14sb\_parmbsc1\_modHIH.ff/aminoacids.hdb:2 6 HAA1 CAA C2A CBA  
> amber14sb\_parmbsc1\_modHIH.ff/aminoacids.rtp: HAA1 HC 0.01500 23  
> amber14sb\_parmbsc1\_modHIH.ff/aminoacids.rtp: CAA HAA1

> grep “HAA1” minsys.gro  
> 3HIH HAA1 29 -0.575 0.306 4.823

Could you help me understand what I am doing wrong?

Thank you very much,

Salome

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 22, 2021, 12:39pm UTC](https://gromacs.bioexcel.eu/t/atomname-problem-while-adding-a-residue-to-a-forcefield/2012/2 "2021-04-22T12:39:40Z")

</div>

> [@s\_llabres](#):
>
> amber14sb\_parmbsc1\_modHIH.ff/aminoacids.hdb:2 6 HAA1 CAA C2A CBA

This is your issue right here. You’re telling `pdb2gmx` to add two H atoms, with base name HAA1, to your structure. This causes `pdb2gmx` to create HAA11 and HAA12 to the structure, which are then not found in the `.rtp` entry.

---

<div class="post-metadata">

**Author:** ![s\_llabres](https://avatars.discourse-cdn.com/v4/letter/s/c2a13f/32.png) [@s\_llabres](https://gromacs.bioexcel.eu/u/s_llabres)\
**Post date:** [April 22, 2021, 12:41pm UTC](https://gromacs.bioexcel.eu/t/atomname-problem-while-adding-a-residue-to-a-forcefield/2012/3 "2021-04-22T12:41:17Z")

</div>

> [@jalemkul](#):
>
> ’re telling `pdb2gmx` to add two H atoms, with base name HAA1, to your structure. This causes `pdb2gmx` to create

Thanks a lot, Justin.

Salome