Hi,
I have been looking around for ways to insert various monomers of an AMP in membrane bilayers. To start-off, I have been using Charm-Gui, but it seems that I can only insert one peptide at a time in order to run the MD in Gromacs. How can I build patch with various monomers of a peptide inserted in a membrane bilayer (programs? online servers?). I also tried inserting various copies of my peptide in pymol, but because they have the same coordintates this strategy did not work....
Dear Brandt Bertrand ,
Not sure it may help you, but did you come across the following papers?
Crowet, J. M., Nasir, M. N., Dony, N., Deschamps, A., Stroobant, V., Morsomme, P., ... & Lins, L. (2018). Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study. International journal of molecular sciences, 19(9), 2772.
And
Fontana, F., & Gelain, F. (2020). Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides. Nanoscale Advances, 2(1), 190-198.
The second one includes quite some details in the supplementary information (see also enclosed).
Hope this helps you any further.
Best regards.
Thanks a lot Rob, Keller, I will take a looks at the papers you suggested to see if I can get around the problem.
Kind regards.
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