# Gmx rms output in pdb

**URL:** <https://gromacs.bioexcel.eu/t/gmx-rms-output-in-pdb/226>\
**Category:** User discussions\
**Created:** [June 1, 2020, 4:21pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-output-in-pdb/226 "2020-06-01T16:21:22Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Neena](https://avatars.discourse-cdn.com/v4/letter/n/bc79bd/32.png) [@Neena](https://gromacs.bioexcel.eu/u/Neena)\
**Post date:** [June 1, 2020, 4:21pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-output-in-pdb/226/1 "2020-06-01T16:21:22Z")

</div>

GROMACS version: 2018.4  
GROMACS modification: No  
Here post your question

How can I view the aligned structures (after LSQ fitting of structures in a trajectory) on gmx rms in a pdb format?

---

<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [August 4, 2020, 10:43am UTC](https://gromacs.bioexcel.eu/t/gmx-rms-output-in-pdb/226/2 "2020-08-04T10:43:24Z")

</div>

Hi,  
you can use [gmx confrms](http://manual.gromacs.org/documentation/current/onlinehelp/gmx-confrms.html). Tool generates a pdb file that contains the 2 aligned structure.