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I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot see the ligand. How do I select the heteroatom in the graphical representation window? My complex has 1129 + 50(ligand atoms) but while loading it just shows the protein molecule(1129).

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-> – Lo Sauer May 26 '13 at 7:23

After you load the molecule in VMD, from the menu bar select Graphics->Representations... In the box labeled Selected Atoms, type "hetero" and hit enter. You should now see only your ligand (and whatever other non-protein/DNA atoms that happen to be in your PDB file). Hit the Create Rep button, enter "protein" in the Selected Atoms box and hit enter (you can see a list of all the possible selection words in the Selections tab). You will now have a separate representation for your protein and your heteroatoms, and you can modify them with the other settings in the Graphical Representations dialog in order to make them visually distinct from one another.

If this doesn't fix your problem, open up your PDB file in a text editor and check to make sure that there are lines that start with ATOM or HETATM that correspond to the atoms in your ligand. If they aren't there, your problem isn't with VMD but with one of your prior manipulations.

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