Constructing protein+bilayer with Insane

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P_Banerjee
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5 years 4 weeks ago #8068 by P_Banerjee

Constructing protein+bilayer with Insane was created by P_Banerjee

Hello Martini community,

I want to attach a protein to a lipid to further insert the resulting construction into a bilayer. Is this possible with insane.py? If yes, how so?

Thanks in advance!

Best,
Pallavi Banerjee

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riccardo
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5 years 3 weeks ago #8069 by riccardo

Replied by riccardo on topic Constructing protein+bilayer with Insane

I'm not an expert about insane and there's probably multiple way of achieving this. What I can think of is the following: first of all, I'm assuming you mean that the lipid is covalently bound to the protein. If so, just make a martini model for the protein (see martinize), take from the lipidome your lipid model (or, if you need a lipid which is not present in the Martini lipidome just pick the most similar and adapt it), and merge the two itps according to the structure you need. Then use the resulting protein-ligand complex as input for insane.

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P_Banerjee
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5 years 2 weeks ago #8078 by P_Banerjee

Replied by P_Banerjee on topic Constructing protein+bilayer with Insane

Hi Riccardo,

Yes, I managed to merge the structure files of the protein and the lipid by playing around with the positioning of the molecules, so that the protein was close enough to the lipid to form a covalent bond as detected from the merged itps. And then used martinize, as you suggested.

Thanks!

Best,
Pallavi

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Constructing protein+bilayer with Insane