[gmx-users] Problem with Inflategro!!!

[Manikam Sadasivam Saravanan]

Hi,

I am a new user to Gromacs, just started exploring it since 3 months, Thanks
to Justin, In-fact i learned a lot form his tutorial using KALP protein in
dppc.

Currently I am working with simulation of Membrane protein in a popc
bilayer, its a complete membrane protien which lies in one of the leaflet of
the bilayer. I placed my protein inside the popc bilayer (developed using
Charmm GUI) in the exact position using SYBYL , same as what is done in the
"building unit cell" part of the KALP tutorial and with the satisfied
orientation of protein.
Then the final pdb with protein, popc and water molecules is used to produce
a .gro file using pdb2gmx tool.

later I tried to do "Inflategro" to remove the unwanted lipid molecules
interacting with my protein, but i was not successful because, when i
visualize my .gro file of system-inflated, my water molecules are still
present and my protein is out of from my lipid box and when i shrink the
bilayer, the protein is completely lost!
could you please give me an idea to do a proper inflated and deflate in my
case?  thank you!!
~Saravanan









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MSS