normal I need help with domELNEDIN. >.<

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10 years 3 weeks ago #3928 by yipy0005
I need help with domELNEDIN. >.< was created by yipy0005
Hi, i saw on this page: users-birc.au.dk/leat/domELNEDIN/ on how to generate the topology for domELNEDIN. What I wish to ask is, with this topology, do I still have to run minimization, npt, nvt, and dynamic simulations? If not, what do I do with it?

Thanks.

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10 years 3 weeks ago #3930 by Clement
Replied by Clement on topic I need help with domELNEDIN. >.<
"domELNEDIN" is strictly the same as ElNeDyn. Doesn't add or remove anything. Proceed as usual.

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10 years 3 weeks ago #3932 by yipy0005
Replied by yipy0005 on topic I need help with domELNEDIN. >.<
Thanks for the prompt reply. I read from elsewhere that the ELNEDIN model doesn't allow conformational changes and domELNEDIN model does. So if you said that both are technically the same, does that mean the trajectory I obtained from ELNEDIN = domELNEDIN?

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10 years 3 weeks ago #3935 by Clement
Replied by Clement on topic I need help with domELNEDIN. >.<
None of them allow secondary structure changes; following the Martini force field philosophy. What they really mean is that you can observe changes in the contact surface between two subunits of a protein if they're are not linked together and restrained by an elastic network.

In fact, it just depends on how you define the elastic network in the first place: for each of your subunits separately or for the entire protein. If no strings are linking the two subunits, you'll observe "conformational changes" and slight modification of the interactions between them.

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10 years 3 weeks ago #3939 by yipy0005
Replied by yipy0005 on topic I need help with domELNEDIN. >.<
So you are saying, if I have 2 units within 1 protein and I don't apply elastic network (the "string") to them, I will observe conformational changes when viewing the CG trajectory?

What I'm actually trying to do now is I wish to see the internal dynamics of a large protein (E.g. PPAR) where I hope to see more intense movements between the helices. I tried the AA approach, but due to the time scale, there's absolutely no way to visualize such internal motions. That's why I'm resorting to CG and ELNEDIN. So if I apply ELNEDIN throughout the whole protein, what are the chances I will get to see the more intense internal dynamics of the protein?

Thanks. =)

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10 years 3 weeks ago #3941 by Clement
Replied by Clement on topic I need help with domELNEDIN. >.<
I'd advise not to put strings between subunits in proteins in general, i.e. define and apply ElNeDyn on each subunit separately.

What do you mean by "see more intense movements between the helices"? Remember you're using an elastic network...

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10 years 3 weeks ago #3942 by yipy0005
Replied by yipy0005 on topic I need help with domELNEDIN. >.<
Okie, if I understood you correctly, I'm rephrasing the idea into an example:

I have protein with 2 subunits, so if I want to see if they interact, then it's advised I "strung" them up in each subunit but not between them, and with the time scale advantage provided by CG, I may just be able to observe some conformational changes BETWEEN the 2 subunits, and not within.

So now, instead of a protein with 2 subunits, I have a protein that consists of let's say, 20 helices linked from N- to C-terminus. Using an AA approach, it would take me ages to obtain a simulation whereby I see the helices interacting with each other within the protein. So, in this case, since it's a time-scale problem, do I simply run it using CG without ELNEDIN?

Hopefully, I ain't confusing you too much with the way I phrase. >.<

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10 years 3 weeks ago #3943 by Clement
Replied by Clement on topic I need help with domELNEDIN. >.<

I have protein with 2 subunits, so if I want to see if they interact, then it's advised I "strung" them up in each subunit but not between them, and with the time scale advantage provided by CG, I may just be able to observe some conformational changes BETWEEN the 2 subunits, and not within.

That's it.

So now, instead of a protein with 2 subunits, I have a protein that consists of let's say, 20 helices linked from N- to C-terminus. Using an AA approach, it would take me ages to obtain a simulation whereby I see the helices interacting with each other within the protein. So, in this case, since it's a time-scale problem, do I simply run it using CG without ELNEDIN?

Either you do that, either you try to remove the elastic network between each helices (keeping the elastic network internal to each helix). But all in all, the effects you want to observe here might be too fine to be seen in CG... To be tested.

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10 years 3 weeks ago #3945 by yipy0005
Replied by yipy0005 on topic I need help with domELNEDIN. >.<
How do I keep the elastic network internal to each helix only?

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10 years 3 weeks ago #3946 by Clement
Replied by Clement on topic I need help with domELNEDIN. >.<
You'll need to write something yourself I'm afraid... A small python script parsing the indices and removing the elastic strings linking different helices from the topology. Shouldn't be too hard to do! ;-)

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10 years 3 weeks ago #3947 by yipy0005
Replied by yipy0005 on topic I need help with domELNEDIN. >.<
O.O -> X.X Can provide me with some clues to proceed with? Haha, I really have no clue. >.<

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