In the current daily build (and for future releases) we have built in more protections so that if there are no hydrogens and you haven't added them with Chimera, they will still be added by the AutoDock prep scripts before the docking calculation. Polar hydrogens are needed for Vina to correctly recognize the atom types, to correctly calculate docking scores. However, there is no corresponding option for the ligand in that interface: instead, you need to add hydrogens to the ligand beforehand, for example with Chimera AddH. For the receptor, this is generally taken care of because the "add hydrogens in Chimera" option in the AutoDock Vina interface is turned on by default. Namely, change the name of delta-protonated histidines to HID, epsilon-protonated to HIE, and doubly-protonated to HIP, then use 'useHisName true' in the addh command. To protonate water and yet preserve current histidine protonation you will have to get tricky. Users of the AutoDock Vina interface in Chimera 1.7 should be aware of a potential "gotcha": the structures should include hydrogens, at least the "polar" (potentially H-bonding) ones. addh will always add hydrogens to the entire model(s) specified. Next message: python script running OUTSIDE chimera possible?.Previous message: Tube representation of the motion projections along the eigen vectors.AutoDock Vina and hydrogens Elaine Meng meng at
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