Re: [AMBER] parmed for two atom type with the same LJ parameters

From: Jason Swails <>
Date: Thu, 14 Oct 2021 16:29:14 -0400

On Thu, Oct 14, 2021 at 11:44 AM Song, Lin <>

> Hi Qinghua,
> One thing you may try is changing one of the metal ion’s atom type to
> something new:
> addLJType .%OIMD
> And you might need to add the polarizability of the new atom type, which
> should have the same value of the metal ion’s atom type.
> My two cents. Please correct me if I’m wrong.

addLJType is precisely how you do this. The only comment I'll add is that
the first command (`change AMBER_ATOM_TYPE`) is not necessary (although
naturally the mask in the second command will need to change accordingly).

As the OP pointed out, Amber condenses Lennard-Jones types differently than
atom types (it does not use the AMBER_ATOM_TYPE designation). As such, you
can actually use `addLJType` to give an atom a separate set of
Lennard-Jones parameters without adjusting any of the other atoms of the
same type.

All the best,

Jason M. Swails
AMBER mailing list
Received on Thu Oct 14 2021 - 14:00:02 PDT
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