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ccsb-scripps / AutoDock-Vina

AutoDock Vina
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Amides in macrocycles #170

Closed pwging13 closed 1 year ago

pwging13 commented 1 year ago

It seems as thought amides are not held to a planar geometry when they are part of a macrocycle. 6 and smaller member rings seem to be fine, but 7 and up give me rotated amide bonds unless I use --rigid_macrocycles while preparing ligand pdbqt files.

Is this a known issue? I tried using the --rigidify_bonds_smarts flag while preparing ligands to rigidify all amides (which should be the default behavior I thought), but that flag gave me trouble.

Any work arounds?

diogomart commented 1 year ago

Amide bonds are made rotatable only when the amide nitrogen has two non-hydrogen substituents and those substituents are different. While this lead to non-planar amides, which is bad, it allows both planar conformers to be sampled. Whether or not the amide N-C bond is part of a macrocycle does not affect the rotatable/non-rotatable status. To always keep amides rigid, use: --rigidify_bonds_smarts "O=[CX3][NX3]" --rigidify_bonds_indices 2 3 If this doesn't work, or if I misunderstood the problem, please provide an example so I can reproduce the issue.