[gmx-users] Constraints and ligands

[P.R.Anand Narayanan]

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?

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? 

Regards,
Anand




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