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I'm trying to reproduce this tutorial: http://www.mdtutorials.com/gmx/lysozyme/04_ions.html but with a different protein.

During the step of adding ions (using genion for ion.tpr file generation)I get the 'No such moleculetype SOL'. When I add the SOL in the moleculetype section, I get 'Moleculetype 'protein' has no atoms'.

Any help is appreciated!

I'm providing the relevant parts of topol.top file.

[ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb ...

[ moleculetype ] ;name nrexcl protein 3

[ atoms ] ... ...

[ system ] protein in water

[ molecules ] ; Compound nmols protein 1
SOL 53832

rosanna
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  • Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. – Community Sep 21 '21 at 12:54

1 Answers1

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About SOL error-It seems like your topol.top does not have water topology file. Add line anywhere in topol.top and remove SOL from moleculetype section. #include "oplsaa.ff/spce.itp"

About protein error- Check if your *.gro file include 1 protein molecule and 53832 water molecule in it. I am suspicious your *.gro file does not have protein molecule and filled with water only. Make sure the number of molecules in topol.top should be same with in the *.gro file.

user_sej
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