# Conversion of ligand pdb to gro file

**URL:** <https://gromacs.bioexcel.eu/t/conversion-of-ligand-pdb-to-gro-file/4334>\
**Category:** User discussions\
**Created:** [June 22, 2022, 1:39am UTC](https://gromacs.bioexcel.eu/t/conversion-of-ligand-pdb-to-gro-file/4334 "2022-06-22T01:39:12Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Rishav](https://avatars.discourse-cdn.com/v4/letter/r/74df32/32.png) [@Rishav](https://gromacs.bioexcel.eu/u/Rishav)\
**Post date:** [June 22, 2022, 1:39am UTC](https://gromacs.bioexcel.eu/t/conversion-of-ligand-pdb-to-gro-file/4334/1 "2022-06-22T01:39:12Z")

</div>

GROMACS version: 2022.1  
GROMACS modification: No  
Here post your question

I have a ligand pdb file for flavin adenine dinucleotide (FAD) that I am trying to convert to the gro format using gmx editconf -f fad\_ini.pdb -o fad.gro  
The gro file is truncating the z coordinates of the pdb file and I can’t fix it.  
My z coordinates are xx.xxx 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:** [June 22, 2022, 12:21pm UTC](https://gromacs.bioexcel.eu/t/conversion-of-ligand-pdb-to-gro-file/4334/2 "2022-06-22T12:21:38Z")

</div>

Hi,  
In the gro file, the positions are in nm, (with 3 decimal places) while in pdb the positions are in Angstrom. Can this explain the truncation you observed?  
Here you find more on gro file  
[https://manual.gromacs.org/current/reference-manual/file-formats.html#gro](https://manual.gromacs.org/current/reference-manual/file-formats.html#gro)  
\Alessandra