Category Archives: chemistry

VMD Selection for a Given Docking Box

Docking programs like AutoDock Vina and Schrödinger’s Glide typically require users to specify a docking box. VMD is a popular program for molecular visualization. I often want to visualize the receptor atoms that fall within a given docking box in VMD. This little app generates the VMD selection of these atoms.

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Creating a periodic box programmatically in VMD, with an explicitly specified center

I recently wanted to see if steric clashes at the boundary of a molecular system I’m simulating might be responsible for high-velocity errors. I didn’t want to download the models with the periodic boundary specified because they are enormous, so I discovered how to explicitly specify a periodic box in VMD. My periodic box was […]

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Online SMILES-to-3D visualizer

Click and drag the molecule to rotate it. Enter a new SMILES string using the text box below.

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View amino acids and nucleic acids in 3D

Click and drag the molecule to rotate it. Select a new molecule using the buttons below.

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