Justin<br><br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Sure, you could do all of it within a shell script that loops the commands and checks the printed output.</blockquote><div><br>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 :)<br>
<br><br>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)<br>
<br>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<br>- Changing vdv radii for the C atoms- So i've copied <font face="Arial"><font size="3"> vdwradii.dat</font></font> 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 <font face="Arial"><font size="3"> vdwradii.dat</font></font>? 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 :) )<br>
<br><br>- 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 ?<br><br>
<br>Thank you for your help,<br><br>James<br><br><br></div></div>