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

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Thu, 14 Oct 2021 14:27:33 +0200


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
(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,

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Received on Thu Oct 14 2021 - 05:30:01 PDT
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