Use in PEGylated protein workflow of polyply about coby HOT 2 OPEN

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

from coby.

@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

from coby.