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 <david.case.rutgers.edu> 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
>
>
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>
--
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678
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Received on Fri Oct 26 2018 - 04:30:04 PDT
