[gmx-users] Topology parameters for ligand

[tasneem kausar]

Dear all

I am following Justin's tutorial methane in water for free energy
calculation. I am using Gromacs-5.1.4. The charges of methane in topology
are set to zero. So following the same protocol, is it relevant to set the
charges at zero in topology of the drug. I am confused because in tutorial
of Sander (ethanol in water) charges are present in the topology file.

Please tell me the difference in both the tutorials and how can I apply it
to drug that I want to study.


Thanks in Advance