Hi Amber users,
I am interested in using the membrane builder for new ionizable lipids not currently standard in packmol-memgen.
Right now, I have generated .pdb and topology files (.prm, .itp) for each new ionizable lipid using CGENFF, and currently run self-assembly simulations in GROMACS with the CHARMM36 (July 2022) forcefield.
Alternatively, I am interested in trying prebuilt membranes and thus looked into packmol-memgen (AmberTools23). I am wondering how can I include lipids that aren’t already in memgen.param or pdbs.tar.gz?
Let’s say my new lipids are called “L1” and “L2”. What files would I need for L1 and L2; would a .pdb and .prm & .itp (for topology) suffice? How can I adjust memgen.param and/or other files to incorporate new lipid components into packmol-memgen? What would my ultimate command look like for membrane generation, something like this?
packmol-memgen --lipids L1:L2:POPC:CHL1 --ratio 1:1:1:1 --preoriented --salt --salt_c Na+ --saltcon 0.15 --dist 10 --dist_wat 15 –charmm
Any insight would be greatly appreciated.
Thanks,
Evan
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Received on Tue May 07 2024 - 11:00:02 PDT
