[AMBER] Simulation of protein immobilization

From: Markowska <markowska.kar.gmail.com>
Date: Thu, 29 Jul 2021 14:13:36 +0200

Dear Amber Users,

I'm trying to run a simulation of a protein that is immobilized on a layer.
What I actually want to observe is how the protein sits on that particular
layer. So I followed a tutorial about ASMD
http://ambermd.org/tutorials/advanced/tutorial26/section2.html however I
feel like I'm stuck.
In the dist.RST.dat files I have defined
        iat=19111,1595, --> ID of atom from the protein and ID of atom from
the layer
        r2=13, --> distance between the atoms at the beginning of the MD
        r2a=11, --> distance between the atoms at the end
        rk2=7.2, --> force constant

And so, I have the following questions:
1. Is ASMD a correct way to simulate protein immobilization on a layer? I
want to observe protein sitting on top of the layer. Or should I use some
other technique?
2. Can I define the iat parameter as a set of atoms comprising the protein
and a set of atoms comprising part (or whole) layer?
3. I needed to put some restraints on the layer, can this disturb the ASMD
simulation? Since one of the atoms defined in the iat parameter is
4. How to determine the value of the force constant? 7.2 was the value used
in the tutorial, but I haven't seen further comments on the chosen value. I
tried to increase the energy value, but I did not see any differences.
5. Do you know any papers about such simulations? (I searched for 'protein
immobilization simulations' but without success).

I'll appreciate any help :)
Best regards,
Karolina MitusiƄska PhD
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Received on Thu Jul 29 2021 - 05:30:02 PDT
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