[gmx-users] Protein-Ligand Interactions

su sun.iba2 at gmail.com
Thu Aug 6 23:23:53 CEST 2015

I have posted this query already but in absence of any suggestion,i am posting it again. After completion of protein-ligand MD, I tried to visualize the trajectory in VMD.It shows only protein and my ligand is absent. To view hydrogen bond interactions between pro-lig, i have gmx hbond, that showed the number of donors and acceptirs but again visualising problen. Can anyone help me to know how to view the protein and ligand together and the interactions between them. Or is it this way only that in md.gro file and the md_0_1_noPBC.xtc, no ligand is present? 
Best regards

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