Dear gromacs users,
In order to analyse the adsorption process of a Protein (amphipatic protein)
into a POPC membrane i’m placing several conformations at different distances
of respective membrane (on different simulations) and performed regular MD
simulations.
My problem is that during the production phase the protein start to move
randomly, loosing its amphipatic nature (and in that way, moving far from the
POPC hydrophobic interface).
So, my question is: Is there a way to maintain the tertiary structure
('overall’) of the protein (in my particular case, two alpha helices joined by
a loop) allowing it to maintain its amphipatic nature during the simulation,
helping it to interact peripherally to the hydrophobic interface of the
membrane?
In any case, maybe this is not the ideal strategy to analyse the interaction
between this two macromolecules (protein interacting peripherally with respect
to a bilayer membrane), so if you think in something else please feel free to
make any suggestions.
Best regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 71 2 201<tel://T:%20(+56)%2071%202%20201> 798
E: c<mailto:[email protected]>[email protected] or
[email protected]<mailto:[email protected]>
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