Dear All,
I am using AmberTools for my research - specifically AmberTools25.
I am writing because I had a question about AMBER Lipid21. I am trying to source AMBER parameters for three lipids: SLPC, SAPI and OSM.
* 1-stearoyl-2-linoleoyl-sn-glycero-3-phosphocholine (SLPC),
* 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphoinositol (SAPI),
* N-oleoyl-sphingomyelin (OSM),
I have developed a fragmentation protocol that cleaves the lipids, calculates AM1-BCC charges on methyl-capped sub-components, and splices them back together. I then route the Ewald remainder to the polar headgroups to preserve the hydrophobic tails, and assign the missing bonded parameters via GAFF2.
An initial 500 ns simulation of a 96-lipid bilayer using these parameters shows the area per lipid profiles maintain a clean unimodal distribution. I would greatly appreciate your thoughts on the validity of this fragmentation/GAFF2 procedure for a publication. Are there any known pitfalls with this approach that I should be cautious of, or is there a recommended alternative for these specific lipids?
I hope this is clear and I look forward to your replies.
Best wishes,
Ben
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Received on Thu Jul 02 2026 - 06:00:02 PDT
