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<p id="">Dear Gromacs Users,</p>
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<p>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.
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<p>That sounds ok in terms of hydrophobicity.</p>
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<p>However, maybe I should run simulation with constrained backbone and coiled coil? What do you think?</p>
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<p>Regards,</p>
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<p>Jan</p>
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<div><font face="Arial" size="2">===========================================================</font></div>
<div><font face="Arial" size="2">Jan Marzinek<br>
PhD Candidate<br>
Centre for Process Systems Engineering<br>
Department of Chemical Engineering<br>
Imperial College London<br>
South Kensington Campus<br>
London SW7 2AZ<br>
E: </font><a href="mailto:j.marzinek10@imperial.ac.uk"><font face="Arial" size="2">j.marzinek10@imperial.ac.uk</font></a><br>
<font face="Arial" size="2">M: +44(0)7411 640 552</font></div>
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