James, As the consequence the correct orientation of the peptide in the membrane as well as futher solvation are caused many questions :)
Firsly, following by tutorial guide I've done orientation of KALP peptide in the membrane by 1- perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat 2- minimization 3- perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat 4- minimization after six iterations of the 3rd and 4th steps I've obtained 6,5 nm^2 value for the area per lipid Next I've done solvation of my protein ( including big vdv radii for carbons ) Finally my sytem is consisted of 70000 atoms. I think that it's too big ammount of water molecules for such small protein like KALP so its seems that i've done some mistakes- 1- During shrinking of my peptide- I think that obtained structure (http://www.sendspace.com/file/wenkf4) consist of too big distances beetween peptides so it should be futher shrinked. But how many iterations must be? I've found in the tutorial that 65 A^2 is good value for that system. But maybe I've used wrong parametries in the pl program? 2- Or maybe too many waters are moved within the membrane in spite of increased VDV radius for carbon atoms. So what I should do for the excluding all unnecessary water from my structure? E.g I want to simulate hydrophobic effect. What length of that simulation must be ? How I can evaluate the ammount of water before and after simulations? Finally, What other options of Genbox could I use for preventing insertion of water into my membrane ? Thank you for your help, James
-- 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
