Pmx and protein structure water molecules

pmx
1

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

2

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

3

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

Raitis