PEGylated lipid bilayer containing MARTINI 3 cholesterol.

[ohyh]

polyply version 1.4.0 polyply gen_coords -p system_10.top -o 2k_010.gro -c memb.gro -res PEO OHter -name test -box 15 15 20 -split DPPE:HEAD-NH3:TAIL-PO4,GL1,GL2,C1A,C2A,C3A,C4A,C1B,C2B,C3B,C4B

Expected behavior Hi Polyply team,

I was trying to generate PEG chains on the membrane including cholesterols. I got configuration with two problems - 1) PEG chains imbedded inside of the membrane, and 2) floating cholesterol out of the membrane. I assume MARTINI3 cholesterol is recently release, and Polyply hasen't been updated? Please, take a look into the files that I uploaded.

Additional Files If applicable, add all files needed in the reproduction. tmp.zip

[fgrunewald]

@ohyh thanks for raising this issue. The reason for the free floating cholesterols is easy to identify: Your topology specifies 216 Cholesterol molecules but in the memb.gro file there are only 192 Cholesterol molecules present. Thus polyply constructs the missing molecules and will just randomly place them. If you fix the Cholesterol in your topology file this should not happen anymore. Be aware to reduce the number of molecules for the correct leaflet.

The reason for the PEG going inside the membrane is likely due to the fact that your membrane is not equilibrated. There is simply too much space between the lipids. To fix this you can simply provide a build file, which specifies that there should be no PEO inside the membrane. In your case the following file does the job:

[ molecule ]
PGL2k 0 36
[ rectangle ]
; resname start stop in/out x y z a b c
; for syntax see wiki
PEO        2     47 out  10.0 10.0 10.0 10.0 10.0 1.5

The syntax for the build file is explained here in the wiki. The polyply command then becomes:

polyply gen_coords -p system_10.top -o 2k_010.gro -c memb.gro -res PEO OHter -name test -box 15 15 20 -split DPPE:HEAD-NH3:TAIL-PO4,GL1,GL2,C1A,C2A,C3A,C4A,C1B,C2B,C3B,C4B -b build_file.bld

Also please keep in mind that PEG currently doesn't work well with Martini3 lipids. The current workaround is to scale PEG water interactions at the expensive of making PEG more hydrophilic of course.

[ohyh]

Hi, thanks for the quick response. All issues are resolved. Thank you.

[fgrunewald]

@ohyh I'm happy to help and good to hear that it worked. By the way there are 9 beads per cholesterol in the Martini three model. Hence the accounting mistake. ;)

[ohyh]

Yes, that's what I found, so I edited my reply :)