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

From: Maghsoud, Yazdan <YazdanMaghsoud.my.unt.edu>
Date: Fri, 4 Jun 2021 23:12:45 +0000

Dear Amber users,

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?

Thank you all in advance
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Received on Fri Jun 04 2021 - 16:30:02 PDT
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