Is there a manual method to create hydrogen bonds

Started by bendbob

bendbob Lv 1

I know moving the parts closer together will automatically create bonds, but, I'm wondering if I can click/drag on an atom (blue) to another atom(red) and the bond is created?

xiando Lv 1

Hydrogen bonds are created by proximity. That is, the atoms have to be close enough to form the bond, so if they're not, no bond will form.

infjamc Lv 1

The short answer is no. However, there is a workaround that might produce the results you're looking for:

  1. First, Go into full-atom mode by pressing Ctrl+Shift+V.

  2. Place a band between the two atoms between which you want to form a hydrogen bond, then set its length to zero. (It might be wise to place a few extra bands on the other atoms on the side chain/backbone segment involved just to be safe.)

  3. Freeze everything except for the side chains/backbone segments involved in the hydrogen bond.

  4. Use a recipe to increase the band strength to 10. The result should look like the screen shot shown on the left. (This step is critical, as the atoms involved might otherwise not move at all.)

  5. Wiggle. If you've done steps 2-4 correctly, the segments you're trying to manipulate should be forced into the direction specified by the bands. If this step results in other parts of the protein being moved out of place, undo and add extra bands to "anchor" the rest of the protein

  6. Exit full-atom mode by pressing Ctrl+Shift+M.