Justin
Sure, you could do all of it within a shell script that loops the commands > and checks the printed output. As I understood in that iterations only step with scalling by factor 0.95 and futher energy minimization must be included until desired S per lipid will be reached. Could you provide me with a small example of such script for better understanding of the syntax. I've never done unix's shell scripts before :) Could you tell me where I could found experimental valuee for Area per lipid for differen cases (e.g I'll be work with large membrane proteins such as membrane receptors so i wounder to know what values of S per lipid as well as S per protein I might expect in that case) Also I have a question about solvation of my membrane protein via GENBOX. I found 2 possible ways to exclude water from the insertion into membrane - Changing vdv radii for the C atoms- So i've copied vdwradii.dat to my work dirrectory and changed vdv R. How I should to define that genbox uses exactly that modified file located in my working directory instead of default vdwradii.dat? Finally how I can check that there are not waters within the membrane ? (I've tried to visualize via VMD but the overal picture is very unclear :) ) - Also I've found that I can Running short md to exclude those waters via hyfrophobic effect. What parametries would be opti,al for that simulation in case of KALP as well as other more larger proteins ? Thank you for your help, James
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