Membrane protein

[d-beltran]

Hi,

I have to search pockets in membrane proteins.
I don't want mdpocket to find pockets in the membrane.
I can't remove the membrane since I don't want mdpocket to find pockets where the membrane is either.
Which is the best approach to solve this situation?

I have played with the -c, -k and -a options but I am not sure if they work as I need or if they just remove the membrane. It is hard to see by eye since when I run mdpockets with the membrane I also see small pockets between the protein and the membrane.

Thank you for your time :)

[pschmidtke]

Not sure this is somehow possible now. What would be needed is a flag to specify for instance what alpha spheres to drop if they overlap with particular residus / atoms.

Is it a simple POPC membrane or a jolly mix of different lipids?

[d-beltran]

Thank you for your fast reply :)

Is it a simple POPC membrane or a jolly mix of different lipids?

I have to work with both situations

By now, I will run mdpocket without the membrane and then I will find out which grid points are overlapping with the membrane somehow. I look forward to use this new flag.

Cheers