[email protected] wrote:
Dear All,
I'm a new comer to gromacs. I need to perform molecular dynamics
simulation of my protein within the POPC membrane. I have downloaded the
128a popc lipid from Prof.Tieleman's group along with the required
popc.itp. My protein of interest is 458 residues. Since the 128a popc is
already Simulated for 1600 ps, i haven't done membrane only simulation. So
i directly aligned my protein with the membrane using VMD and have saved
the coordinates. However after i aligned my protein with the membrane, i
felt the membrane was not big enough for my protein of interest, also, the
N-terminal region and the loop regions in the C-terminal region and
stretching outside water molecule above and below respectively.ow, i have
two questions here...
Yep, if the protein is sticking "out" of the box on both sides, the box is too
small.
1. How would i increase the number of lipids from the existing one?
Two options:
1. genconf -nbox will give integer multiples of the lipid system (i.e., -nbox 2
2 1 will expand the bilayer in the x and y directions and give 512 lipids)
2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit finer
control over how large the box is and how many lipids will result.
2. Also, i should increase increase the number of water molecules above
and below the membrane so that it covers the whole region of N-terminal
and also the loop regions of the C-terminal.
Expand the box using editconf and add solvent with genbox.
Now, How to perform these tasks??If i do so will it be compatible with the
popc.itp file which i downloaded from the Prof. Tieleman's group?
None of the above operations have any influence on the parameters contained in
popc.itp. If you are unsure about Gromacs workflows, file formats, etc. then
you really need read the manual and do some more basic tutorial material before
you attempt a difficult simulation like a membrane protein. There are a lot of
pitfalls in simulating such a complex system, and if you are not ready for them,
then you can waste a whole lot of time generating nonsensical results :)
3. My third question is while aligning my protein with the membrane should
i make a hole first or after aligning the protein should i remove the
overlapping lipids with the proteins?which one would be better??
There are several methods for doing this. See below.
I have tried out some of the methodologies available in the internet but
it dosen't help me.If anyone of you have a detailed step by step
methodology right from the first step to till running the MD simulation
please let me know.
Saying you've tried things and they didn't work is useless. What did you try?
What links can you provide? Have you tried the membrane protein tutorial linked
from the Gromacs site? That's about as step-by-step as it gets.
-Justin
Your help will be highly appreciated.
Looking forward to hear from you.
Best regards
Padmanabhan
--
========================================
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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