Re: [AMBER] Simulating a covalently bound ligand

From: senal dinuka <>
Date: Fri, 26 Oct 2018 16:33:22 +0530

I need to bond a glycan C atom with a GLU (glutamte) O atom and also a
aglycon O atom with a GLH (glutamic) acidic H
atom. Should I need to change GLU/GLH residue naming according Amber
glycoprotein libraries as mentioned in the tutorials. If so where do I find
such residue naming conventions?

Thank you

On Tue, Oct 23, 2018 at 5:12 PM David A Case <> wrote:

> On Tue, Oct 23, 2018, senal dinuka wrote:
> >
> > I'm simulating a protein-ligand complex in which ligand is bound
> covalently
> > to the protein at 2 amino acids residues namely GLH and GLU. I would like
> > to know whether I am supposed to generate specific parameters for the
> > forming bond or would using bond <atom> <atom> in leap does this for me?
> No: the bond command in tleap just adds the bond to the list of bonds.
> The parameters (i.e. force constant and equilibrium distance) would need
> to entered via a frcmod file, if they are not already present in one of
> the standard parm.dat files.
> Also note: when you add a bond, you are automatically also adding angle
> and torsion terms connected to that bond. Those parts of the force
> field may also need to be specified. Tleap will tell you which (if any)
> parameters are missing, so you can see what you have to add.
> ....dac
> _______________________________________________
> AMBER mailing list

D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
AMBER mailing list
Received on Fri Oct 26 2018 - 04:30:04 PDT
Custom Search