Hi, I used the inflategro.pl script to insert my protein into the membrane and scaled down the lipids until it reached the recommended area per lipid value. After removing 4 lipid molecules, I started with an area of 90 square angstrom and reached a value of 65 square angstrom within just 5 iterations. However, when I had a look at my gro file, all my lipids look spaced out and there seems to be too much of gap between the lipids and the protein such that if I solvate it, I am pretty sure water molecules can easily occupy those cavities.
I am wondering what would have possibly gone wrong?! Cheers Sweta ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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
