[gmx-users] topology file of ligand

[sunyeping]

Dear gromacs users,
 
I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he  immediately notice three things that are wrong with this topology, which include charge group, H atom charge, etc. 
     And the author then reconstructed a topology file.  I don't understand how the charge group and charge of individual atom are correctly assigned. Could you explain it to me? 
 
Thanks.
 
Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences