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
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