I want to generate DOPC:DOPS (9:1) liposome. I found PACKMOL with the input example "Double layered spherical vesicle with water inside and outside" (https://m3g.github.io/packmol/examples.shtml)
I am also open for the other approach.
I have the necessery .pdb files, they are linear to ease the packing process, correctly set hydrophilic/hydrophobic atom, but PACKMOL still cannot converge. Any ideas what is wrong?
tolerance 2.0 add_amber_teroutput DOPC_DOPS_9_1.pdbfiletype pdb# 308 water molecules willfill the interior.structure water.pdb number 308 inside sphere 0. 0. 0. 13.end structure# Inner layer of the liposome (DOPC:DOPS 9:1)structure dopc.mol number 81 # 90 lipids in total, 81 DOPC for 9:1 ratio atoms 14 inside sphere 0. 0. 0. 14. end atoms atoms 55 outside sphere 0. 0. 0. 26. end atomsend structure structure dops.mol number 9 # 90 lipids in total, 9 DOPS for 9:1 ratio atoms 1 inside sphere 0. 0. 0. 14. end atoms atoms 56 outside sphere 0. 0. 0. 26. end atomsend structure # Outer layer of the liposome (DOPC:DOPS 9:1)structure dopc.mol number 270 atoms 55 inside sphere 0. 0. 0. 29. end atoms atoms 14 outside sphere 0. 0. 0. 41. end atomsend structure structure DOPS.pdb number 30 atoms 56 inside sphere 0. 0. 0. 29. end atoms atoms 1 outside sphere 0. 0. 0. 41. end atomsend structure # Finally, 17536 water molecules will form the final solvation shell.structure water.pdb number 17536 inside box -47.5 -47.5 -47.5 47.5 47.5 47.5 outside sphere 0. 0. 0. 43.end structure