James Starlight wrote:
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 <http://inflategro.pl/> confout.gro 0.95 DPPC 0
system_shrink1.gro 5 area_shrink1.dat
2- minimization
3- perl inflategro.pl <http://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
The tutorial suggests at least 26 or so iterations. Your APL value is 100 times
larger than it should be.
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
Yes, because your membrane is not correctly packed.
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.
Correct.
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?
No, you just haven't done enough iterations. See above. Your value is 6.5 nm^2
, which is 6500 A^2.
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?
Ignore this for now. Your system simply isn't built correctly.
E.g I want to simulate hydrophobic effect. What length of that simulation must
be ?
Perhaps tens of ns.
How I can evaluate the ammount of water before and after simulations?
Visualization.
Finally, What other options of Genbox could I use for preventing insertion of
water into my membrane ?
None. A better starting model is required.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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