Dear gmx user
I am Gromacs version 4.6.7 user.
I am working on a protein which has Ub (Ubiquitin) binding domain having strong affinity for Ub.
On one side, protein has ubiquitin binding domain and on the other side of the same protein, alpha-helix attached Ub is located. Now helix-attached Ub acts as a career to transport Ub towards Ub binding domain on the protein. It was demonstrated recently by experimental lab. I want to test by MD simulation. I tried by MD and flooding, but no success. I have chosen appropriate vectors and made sam.edi (Essential dyna sampling input) and performed flooding. I found the configurational changes but no movement obtained on helix (helix attached Ub).
Any idea how could I make a travel alpha-helix attached Ub towards Ub binding domain by MD simulation. or I am wondering to make movement of helix attached Ub a bit of. or This test might not be feasible computationally.
For detail please find model figure from the attachment.
Thank you
Perhaps the new pull code might come in handy. You can now use angular reaction coordinates. You'll probably need to get a newer version of Gromacs however.
Thanks Erik.
Will try and let you know.
Earlier, 5.0 series suppose to be a newer version, right?
Very early 5.0 might lack some bug fixes that were backported to late 4.X. I'd go for latest 5.1, or better still, Gromacs 2016.
Come to think of it, I'm not sure all pull code features are present in early 5.0 either.
How will you determine that the MD-simulated conformational change of the protein is a good model of the actual conformational change? Are there any (experimental data on some) "intermediate" structures along the "helix-movement pathway"?
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