What computational chemistry tool can be best for this time of system, especially that phosphatidylserine and phospatidylethanolamine have interactions in the lipid bilayer?
Since this system is very large for quantum chemistry you should use the molecular dynamics (MD) solutions which is widely used for those systems and produces generally good results. For example you obtain info about lipid per area, lipid order, deuterium order parameters etc. There are many MD programs such as Gromacs(free) or Amber. There is a good tutorial here for amber:
http://ambermd.org/tutorials/advanced/tutorial16/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459508/
If you have however a little more experience in quantum chemistry then you will have even more accurate results using the ONIOM method implemented in Gaussian. It is a hybrid qm/mm method and separates the system into layers according to the computational accuracy. The metal-dppc headgroup wil be your inner layer with a very precise calculation (DFT, MP2) and the outer layer of low interest with molecular mechanics. Take a look there:
http://zhao.lnm.cn/group/pdf/JCIS_hydration.pdf
Thank you so much for the answer, this will really help.
You can try to use "Electron properties calculations: Search for Critical Points" where You can locate bond critical points (3,-1) or "Electron properties calculations: Integration over Atomic Basins" where You can determine electron overlaps at www.chemosophia.com now for free
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