[gmx-users] Making separate topology file for QM atoms (bharat gupta)

Groenhof, Gerrit ggroenh at gwdg.de
Fri May 13 10:47:15 CEST 2016

You need to make one topology for your protein that includes all atoms that you want to treat with QM. If your QM region includes part of the protein and the ligand, you can most easily make one topology with the -merge option of pdb2gmx.


Dear Gromacs Users,

I am interested to know how to create a separate topology file for the QM
atoms of a system. It would be of great help if somebody can explain this.

For my QM system, I need to include the active site residues + ligand.

*Best Regards*


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