Dear Gromacs Users,
I am running the simualtions between ligands (10-30) and protein - coiled coil segment. My ligand is strongly hydrophobic and the hydrohpohobic strand between two monomers is obviously hidden. I found that my proetin is unfloding from terminals, two strands open allowing ligands to come into hydrophobic residues - the helical structure is partly destroyed as well as coiled coil. That sounds ok in terms of hydrophobicity. However, maybe I should run simulation with constrained backbone and coiled coil? What do you think? Regards, Jan =========================================================== Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: [email protected]<mailto:[email protected]> M: +44(0)7411 640 552
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