Re: [AMBER] Simulating a covalently bound ligand

From: David A Case <>
Date: Tue, 23 Oct 2018 07:39:42 -0400

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.


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Received on Tue Oct 23 2018 - 05:00:02 PDT
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