<br>James,<br><br>As the consequence the correct orientation of the peptide
in the membrane as well as futher solvation are caused many questions :)<br><br><br>Firsly, following by tutorial guide I've done orientation of KALP peptide in the membrane by <br>
<font face="Arial"><font size="3"><pre>1- perl <a href="http://inflategro.pl/" target="_blank">inflategro.pl</a> confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat<br>2- minimization<br>3- perl <a href="http://inflategro.pl/" target="_blank">inflategro.pl</a> system.gro 4 DPPC 14 system_inflated.gro 5 area.dat<br>
<br><br>4- minimization<br><br>after six iterations of the 3rd and 4th steps I've obtained 6,5 nm^2 value for the area per lipid<br><br>Next I've done solvation of my protein ( including big vdv radii for carbons )<br>
<br><br>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<br><br>so its seems that i've done some mistakes-<br>1- During shrinking of my peptide- I think that obtained structure (<a href="http://www.sendspace.com/file/wenkf4" target="_blank">http://www.sendspace.com/file/wenkf4</a>) consist of too big distances beetween peptides so it should be futher shrinked.<br>
<br><br>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?<br><br>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?<br>
<br><br>E.g I want to simulate hydrophobic effect. What length of that simulation must be ?<br>How I can evaluate the ammount of water before and after simulations?<br>Finally, What other options of Genbox could I use for preventing insertion of water into my membrane ?<div class="im">
<br><br><br><br><br><br>Thank you for your help,<br><br><br>James</div></pre></font></font><br>