[AMBER] parmed question regarding modifying Lennard-Jones parameters

From: InSuk Joung <i.joung.gmail.com>
Date: Fri, 8 Jan 2016 17:45:03 +0900

I am using prmed to load topology files and running simulations with
openMM. However, I want to change Lennard-Jones parameters for some atoms
(especially zero-radius hydrogens). In case of wild conformational search,
these zero-radius hydrogens cause nasty problems due to electrostatic

Before create openMM's system, I guess I need to modify them by giving tiny
values to both epsilons and sigma.
This is the part of my python script.

prmtop = pmd.load_file('model.prmtop')
# something for changing lennard-jones parameters
system = prmtop.createSystem()

So far, I tried to modify atom.epsilon and atom.sigma in prmtop.atoms, but
it does not seem to work.

I know that I can use interactive parmed and modify the topology file. I
just want to know if there is a possible way in script-level without
modifying the topology file.

InSuk Joung
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Received on Fri Jan 08 2016 - 01:00:05 PST
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