Hello everybody, I hope you're having a good day!
I'm currently working on a small drug design project as part of my Masters degree and am looking at how halogen bonding can improve the affinity of certain drugs to SERT.
Since it's only course project and had little to do with actual research, we do not have many options of actually evaluating the ligands we come up with.
I've played around a bit with Autodock Vina and Autodock4 and ran some simulations, but as far as I know both force fields do not account for halogen bonding.
After asking a few people, I got a tip from a professor that adding a positive point charge onto the surface of the halogen through a dummy atom was a relatively simple trick that normally works pretty well to approximate the electrostatics of a sigma hole.
I have managed to add the dummy atom using Chem3D but I have a few questions about implementing it into autodock:
1. When I calculate gasteiger charges for the ligand, AutoDockTools gets rid of the charge on the dummy atom (which makes sense). I was thinking to just add a positive charge to the dummy in the ligands .pdbqt file manually. Can I do that without messing up my results? And what sort of values would make sense to simulate the sigma holes of Cl,Br, I?
2. I also need to add a new atom type for the 'Du' dummy atom to the force field, which should be easy enough top do via the atomic parameter file. I am just not completely sure how to choose each parameter.
I am assuming to choose a vdW radius (Rii) and atomic solvation volume (vol) of 0 since I want the forcefield to basically ignore everything about the dummy except for electrostatics.
For the H-bond distance (Rij_hb) I was thinking to use 0 as well since its that way for all hydrogens.
What I am really unsure about are the vdW well depth (epsii), hydrogen bind type (hbond) and the bond_index. The only clue that I have here is to maybe choose hbond=2 for a directional H donor since I want it to work basically the same as a hydrogen bond, but I really have no idea.
Any help on this matter would be greatly appreachiated.
Thank you to everyone in advance!
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