# Pmx and protein structure water molecules

**URL:** <https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041>\
**Category:** pmx\
**Created:** [May 24, 2024, 8:05am UTC](https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041 "2024-05-24T08:05:31Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![raitis.bobrovs](https://avatars.discourse-cdn.com/v4/letter/r/c5a1d2/32.png) [@raitis.bobrovs](https://ask.bioexcel.eu/u/raitis.bobrovs)\
**Post date:** [May 24, 2024, 8:05am UTC](https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041/1 "2024-05-24T08:05:31Z")

</div>

Hi, all

I am having some problems with pmx when I want to use it with my protein structure that also contains water molecules.

Everything did run fine when I tried to set up and run the system without co-crystallised water molecules, however, when I tried to use pmx with a system that contains co-crystallised water molecules, I got typical gmx errors like:

> Fatal error:  
> number of coordinates in coordinate file does not match topology.

Is there a specific way how such water-containing protein structures need to be prepared for pmx?

When I create the protein topology files using gmx, the system contains:

> [molecules]  
> ; Compound #mols  
> Ion\_chain\_C 1  
> Protein\_chain\_A 1  
> Protein\_chain\_B 1  
> SOL 27

After the fe.assemble\_systems the water molecules are dropped in the topology file (but are present in pdb file):

> [molecules]  
> Ion\_chain\_C 1  
> Protein\_chain\_A 1  
> Protein\_chain\_B 1  
> MOL 1

Am I missing something here?  
Is there some easy fix, or setting that I am not aware?

Best regards,  
Raitis

---

<div class="post-metadata">

**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [May 24, 2024, 9:07am UTC](https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041/2 "2024-05-24T09:07:06Z")

</div>

The easiest fix would be to manually add “SOL 27” to the end of the topology file

---

<div class="post-metadata">

**Author:** ![raitis.bobrovs](https://avatars.discourse-cdn.com/v4/letter/r/c5a1d2/32.png) [@raitis.bobrovs](https://ask.bioexcel.eu/u/raitis.bobrovs)\
**Post date:** [May 24, 2024, 1:06pm UTC](https://ask.bioexcel.eu/t/pmx-and-protein-structure-water-molecules/5041/3 "2024-05-24T13:06:28Z")

</div>

Thank you. That works just fine.  
I thought that there might be some settings that I was not aware.

Raitis