Distorted peptide bond with new residue

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Thu Jul 05 2018 - 16:18:28 CDT

Hello everyone,

I have been trying to create a new residue topology and add parameters to
it. The topology and parameters work, however when minimizing the structure
the peptide bond connected to the c terminal of the new residue is
distorted so that the peptide bond has a 0 dihedral angle rather than the
180 it is supposed to have. When creating the psf for this molecule, I had
to manually link this residue to the rest of the chain with a LINK patch.
Could the link patch change the type of the bond somehow?

Thank you in advance

Nicholas J. Palmer

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