normal Backmapping quality after a fully flexible simulation

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2 years 10 months ago - 2 years 10 months ago #9118 by dbn4
Hello there

I am trying to resconstruct a structure full atomistic detail after a fully flexible (without any position restrain) cg simulation.
How good should I except the reconstructed structure to be? (given the fully flexible nature of the simulation)
The backmapping tuto here mentions that the structure in the simulation should be http://www.cgmartini.nl/index.php/tutorials/37-tutorial2/314-tutorial-reverse-mapping#:~:text=without%20position%20restrainsrestrained for proper reconstruction using backmapping.
I gave it a try but the structure's secondary structures don't seem properly formed!
Last edit: 2 years 10 months ago by dbn4.

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2 years 10 months ago #9119 by vainikka
I'd imagine your result will depend on two things: The quality of the original CG simulation (if it was garbage, then backwards will also produce garbage), and the inaccuracies in the backmapping routine which, as I've understood, are not very large (then again, I'm not an expert of this topic and could be wrong).

You mention that the "structure's secondary structure' is not proper. What kind of a molecule are you simulating?

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2 years 10 months ago - 2 years 10 months ago #9120 by dbn4
I am simulating a simple protein
Last edit: 2 years 10 months ago by dbn4.

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2 years 10 months ago #9121 by mnmelo
Hi,

When you mention 'fully flexible' do you mean just without position restraints, or also without any restraints keeping the secondary structure? Do the secondary structures seem well kept along your CG simulations?

Also, what I think Petteri was asking was about the overall structure type of your protein. Is it an IDP? Membrane protein? Mostly helical? Mostly sheet? Globular?

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