[gmx-users] Constraints and ligands

[Mark Abraham]

P.R.Anand Narayanan wrote:
> Dear users,
> I just have 2 queries
> 1) Is it safe to use "united atoms" constraint for positional 
> restraining and md simulation of an enzyme docked to the substrate? if 
> yes, what is the KEYWORD to be typed in the mdp file and in what way is 
> it simpler than the "all-bonds" constraint?

Constraints and restraints are distinct concepts in GROMACS. United 
atoms are something else again. Please do some background reading in the 
manual and ask a focussed question then :-)

> 2) How can a chemical ligand be bonded to a protein ie; with what type 
> of bond formation and how are the residues in the protein chosen for the 
> bonding to be done with the ligand?

It can be bonded whatever way makes sense for your investigation, but 
producing a corresponding topology need not be easy, even if suitable 
force field parameters already exist. You will need a thorough knowledge 
of chapter 5 of the manual. As an exercise that will teach you the 
necessary skills, design a .top file by hand for a molecule that is the 
ligand bound to just the relevant residue, ignoring the rest of the protein.

Mark