[gmx-users] Syntax Error when Adding Ions to DNA/ligand complex

Wahl, David M dmwahl at eagles.usi.edu
Fri Aug 31 07:01:39 CEST 2018

Hello GROMACS users,

I am attempting to run a molecular dynamics simulation with DNA complexed with a small molecule.  I have processed the molecule with ACPYPE, using the GAFF, and merged the topology files into a single topology file. However, when I attempt to use the “grompp” command before adding the ions with genion, I get the following error:

Syntax error - File ligand_GMX.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes

Originally in my single, merged topology file, I had the #include command for the DNA chain topologies before the #include command for the ligand topology. This is the order that resulted in the above error.

Whenever I moved the #include command for the ligand.itp file before the #include command for the DNA chain .itp files, the error seemed to have gone away.

Is this a valid fix for the syntax error? If it isn’t, do you have any suggestions?  If it is, why did it matter that the ligand was included before the DNA? Under the [molecules] section I have DNA before the ligand so I’m not understanding why it is the opposite for the #include commands?

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