[gmx-users] grompp protein-ligand complex simulation

Adamu, Aliyu aliyu.adamu.12 at aberdeen.ac.uk
Tue Mar 1 11:06:35 CET 2016

Hi all,

I am trying to run protein-ligand complex MD in Gromacs 4.6.7. Using opls-aa forcefield. I parameterised my ligand using topolbuild. I managed to defined the unit cell and added solvent successfully. But when trying to  run grompp command for addition of ion, I received fatal error: " atomtype Zn2+ not found". I am a kind of confused because my ligand has no any Zn2+ atom. My ligand constitutes of only H, O, C, and Cl atoms.

Again, when I included call directive: #include "ff2cp.itp" generated by the topolbuild in the ligand topology file (ligand .itp), the error massage changed to: Invalid order for directive atomtypes.
Please guid me on how I can fix this error.

Many thanks
Aliyu Adamu

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