You are here
I am writing you in a hope that the following problems will be resolved with your help.
I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.
I am performing Rosetta Ligand docking for a ligand, let 's say A . The ligand A is in contact with both water and water vapor. I have two main quesions and I would really appreciate your help in this regard:
1. Do I need to explicity consider water in my docking as a separate ligand with the ligand A? Or is the implicit solvation in scoring function sufficient?
Dear Sir and Madam,
I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.
I am reading Mr. Baker's paper titled "Computational design of ligand-binding proteins with high affinity and selectivity". In the supplementary data, they used generate_ligens.linuxiccrelease to generate ligand conformers. But I can't find generate_ligens tool in my directory (~/rosetta/bin), also I didn't find any record about it in Rosetta tutorials. Anyone konws where to find it?
Dear sir and madam,
I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command: