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

From: Song, Lin <>
Date: Thu, 14 Oct 2021 15:44:21 +0000

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.



> On Oct 14, 2021, at 8:27 AM, Qinghua Liao <> wrote:
> Hello,
> In my system, I have two metal ions with exact the same LJ parameters (12-6), different atom type names.
> I tried to use parmed to add a C4 term for just one metal ion, but I found that parmed still added the same C4 term
> for both of the two metal ions, even though they are in different atom types.
> (in principle they are the same, but I want parmed to see them as different)
> I guess parmed did it based on the LJ 12-6 parameters, now the trick I did is adding an extremely small part
> (10^-10, like 0.8 -> 0.800000000001) to the epsilon of the other metal ion,
> then I found that parmed considered the two as two different atoms.
> I am wondering whether there is some setting of parmed which can turn off this searching? Thanks a lot!
> All the best,
> Qinghua
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Received on Thu Oct 14 2021 - 09:00:02 PDT
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