[gmx-users] terminal residues come off and fragment

[Chris Gaughan]

Hello all,

I'm simulating the dimerization of two alpha helices.
I ran the energy minimization in vacuo and looked at
the resulting coordinate file (.gro) in PyMol. The
result looks very close to what I expected, however,
there seem to be asterisks where the peptides overlap
and pieces of the terminal residues seem to
have.....fragmented (there are pieces of them between
the two peptides).

Can someone explain this?

Thanks
Chris




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