Use in PEGylated protein workflow of polyply

[fgrunewald]

Hi @MikkelDA,

I've heard from @KasperBuskPedersen that this tool is an improved successor to insane. I'm one of the core developer of the polyply package used for generating Martini polymer systems. One of the things polyply is quite frequently used for is making PEGylated lipids. So far the tutorial recommends usage of Insane. Updating using this tool could be a good chance to update the tutorial and give your tool more visibility. Unfortunately, my time is very limited but if you'd adopt the insane commands to your package, I'd be open to updating the tutorial swiftly.

Let me know!

Cheers, Fabian

[MikkelDA]

Hello Fabian

I would very much be willing to help convert the commands from insane to CGSB. I assume it is only the commands in the tutorial that you linked.

I can see that the commands specify what seems like an exact number of lipids (e.g. POPC:95 POPE:5) which insane also creates. However, those number of lipids are only created by insane due to, what i consider to be, rounding errors present in insane. Those rounding errors have been corrected in CGSB meaning that a different number of lipids would be placed with the corresponding command (in this case, 101 POPC and 5 POPE as CGSB attempts to optimize the number of lipids according to the given area per lipid, while insane simply rounds down the ratios).

CGSB has an insane compatability mode for lipid ratios, ensuring that the number of lipids that are inserted corresponds to the number that insane would insert. It can be activated using the subcommand "lipid_optim:insane", though it only works properly when no proteins are present (which there aren't in your case so it should work fine).

If you instead want an exact number of lipids to be created irrespective of the size of the system, then you can use the subcommand "lipid_optim:abs_val" to ensure that those exact number of lipids are placed.

I have included three sets off commands below showing the "standard" command, a command with the "insane compatability mode" and a command creating an exact number of lipids.

Here are the command translations:

3 - Generating starting coordinates insane.py: python2 insane.py -l POPC:95 -l POPE:5 -o bilayer.gro -dz 15.0 -x 8.0 -y 8.0 CGSB.py: Standard python CGSB.py -membrane POPC:95 POPE:5 -o_sys bilayer.gro -z 15.0 -x 8.0 -y 8.0 CGSB.py: insane.py compatability setting python CGSB.py -membrane POPC:95 POPE:5 lipid_optim:insane -o_sys bilayer.gro -z 15.0 -x 8.0 -y 8.0 CGSB.py: Absolute number of lipids python CGSB.py -membrane POPC:95 POPE:5 lipid_optim:abs_val -o_sys bilayer.gro -z 15.0 -x 8.0 -y 8.0

Here are the command translations:

3.2 - Coordinates for the brush regime insane.py: python2 insane.py -l POPC:75 -l POPE:25 -o bilayer_brush.gro -dz 33.0 -x 8.0 -y 8.0 CGSB.py: Standard python CGSB.py -membrane POPC:75 POPE:25 -o_sys bilayer_brush.gro -z 33.0 -x 8.0 -y 8.0 CGSB.py: insane.py compatability setting python CGSB.py -membrane POPC:75 POPE:25 lipid_optim:insane -o_sys bilayer_brush.gro -z 33.0 -x 8.0 -y 8.0 CGSB.py: Absolute number of lipids python CGSB.py -membrane POPC:75 POPE:25 lipid_optim:abs_val -o_sys bilayer_brush.gro -z 33.0 -x 8.0 -y 8.0

Cheers, Mikkel

[fgrunewald]

@MikkelDA Thanks for the detailed instructions. I'll update the tutorial hopefully this or next week, if everything works well. The number of lipids is not so problematic I just have to adjust the numbers in the top file