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 -- MSS -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
