Could It Be Possible To Define Hydrogen Bond With A Particular Residue In Docking??

Question

[Spandankeshav]

Hello,

I was wondering that is it possible to defined hydrogen bonding of ligands with a particular residue before submitting a job in gold (in Discovery Studio Platform)? Actually, I have one ligand (juglone) and a protein. In protein there is a residue (Leucin at position 32). I would like to dock a ligand in such a way that the two oxygen atoms in a ligand can make hydrogen bonds with the hydrogen atoms in the N terminal end of the Leucine residue. So, is it possible to define previously bonding of ligands to residue in a protein??

Thanks in Advance!

Cheers!

Keshav

Answer 1

[Vladimir Chupakhin]

GOLD can definitely do that, read the documentation.

[Spandankeshav]

Yeah, I tried to find and I read the GOLD documentation as well but couldn't find any ideas regarding what I am looking for. That's why I posted my problem here otherwise, I wouldn't have posted here.

[Vladimir Chupakhin]

Try this http://www.ccdc.cam.ac.uk/support/documentation/gold/5_1/gold/gold.1.133.html#248748