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nilcm10 / md_membrane_env

A simple guide to do MD of lipid bilayers and analyze them
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leap.in file for protien in lipid bilayer #1

Open bokey007 opened 1 year ago

bokey007 commented 1 year ago

Hi Nil,

Thank u so much for this repo, this had help me put things into perspective.

I notice that u have shared leap.in file for the lipid-only system and not for the protein-lipid system.

I was wondering if you could either share the leap.in file for the protein-lipid system and provide some pointers as to what needs to be added in addition to the leap.in file for lipid only system ?

Thanks Sudhir

bokey007 commented 1 year ago

Also, I observed that there is a force field parameterization option in packmol-memgen as well.

Can we just use that instead of using leap and then amber to gromacs transformation with acpype.

bokey007 commented 1 year ago

One last thing how do we define position restraints for lipid-protein system?

it would also be a great help if u could include equi.sh file for protein-membrane system