Re: [AMBER] Adding several Helium atoms to a Lipid bilayer structure in AMBER

From: David A Case <>
Date: Wed, 9 Jun 2021 09:08:40 -0400

On Fri, Jun 04, 2021, Maghsoud, Yazdan wrote:
>I have a lipid bilayer structure (total charge=0), made by CHARMM. I
>could successfully add waterbox and performed the MD calculations for the
>mentioned system. Now, I want to do a new calculation but this time I
>want to add several Helium atoms around my lipid bilayer and then solvate
>the new system (lipid+helium) into the waterbox. 1st. I do not know how
>to distribute helium atoms around the lipid bilayer structure (I should
>mention that I tried to add ions e.g., Li+ into my structure by LEaP and
>then rename the ions to He but faced the error with the force fields when
>wanted to create the .prmtop and .inpcrd files). 2nd, If it's needed to
>parameterize the He atoms, how should I do that?

To add uncharged atoms like He, you would need to use addIonsRand (which
doesn't care if the "ion" is charged or not), or, perhaps better, look at

You should first create a UNIT for He: create a mol2 file with a single
atom that sits at the origin as has no charge; then manually create a
frcmod file with the desired Lennard-Jones parameters, mass, and so on.

In tleap, use loadMol2 and loadAmberParams to load you unit; then you can
give that unit name to the AddIonsRand command. With luck/perisistence, you
should be able to get the prmtop file with He atoms added.

Note that He is very light, so MD might be a problem. You would need to use
a small time step (say dt=0.001) or (if kinetics is not an issue for you)
assign He an artifically large mass to slow it down.

...good luck....dac

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Received on Wed Jun 09 2021 - 06:30:02 PDT
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