On Fri, Jan 8, 2016 at 3:45 AM, InSuk Joung <i.joung.gmail.com> wrote:
> 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
> interactions.
>
> 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.
>
​Possibly because the information is not being flushed back to the raw data
arrays... That's a complication with the AmberParm class -- there are two
places where the data is held and it's difficult to keep them in-sync.
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.
>
Anything in the interactive interpreter can be used at the script level.
So what you want to use is "changeLJSingleType", and you can use that
inside your script as follows:
import parmed as pmd
prmtop = pmd.load_file('model.prmtop')
pmd.tools.changeLJSingleType(prmtop, '@%HO', rmin=0.8,
epsilon=0.05).execute()
system = prmtop.createSystem() ...
If that doesn't work, let me know.
I hope everything's going well!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 08 2016 - 04:00:06 PST
