Hi all thanks for your valuable suggestions. But still i'm not clear. I have tried using the .tpr file with make_ndx but the index group is displayed is similar to that of the one with .gro file. I have manually identified the residues and when i ran the g_mindist with the ligand 0f 18 atoms against the residues of 174 atoms i'm getting contacts ranging from 87 to 40. please help me with stepwise instruction as I cant follow the thing. Thanks in advance
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