I am interested in peptide self-assembly study by MD simulation. The peptide self-assembles into fibrils at low pH. I use Avogadro program build the peptide monomer in an extended conformation. However, I find it difficult to build a large assembly of peptides (20-40 monomers). i) I do not know how far I should place the monomers from one another. Since I am expecting hydrogen bonds between the monomers, the back-bone CO...HN distance should be less than 2Å ? I that case how can avoid overlapping of atoms.
ii) Avogadro crashes when I try to build a large self-assembly (20 monomers).
If you have a single peptide ready, try importing it multiple times into UCSF Chimera and positioning them using the movement mouse mode (maybe at a safe distance ~2nm from each other, avoiding bias in interaction at the beginning of the simulation) and save the coordinates for the next step. The bonds are expected to form during the simulation. Placing them too far away may increase the time of self-assembly. If you're a gromacs user, you could even setup the positions using gmx editconf but using Chimera maybe easier for you.
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