[gmx-users] Constraints and ligands
Mark.Abraham at anu.edu.au
Fri Oct 30 08:43:41 CET 2009
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.
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