Hello Woonghee--
>
> Will psfGen.cisPeptide will be effective after protocol.loadPDB as well?
> For instance,
>
> protocol.loadPDB("template.pdb")
> psfGen.cisPeptide(.....)
> regularize.addUnknownAtoms_new()
>
This will work in the sense that the equilibrium value of the peptide
bond dihedral angle will be changed from 180 to 0 degrees. However,
the snippet, as written will not change the atomic configuration if
the backbone atoms associated with this linakge are present in
template.pdb.
The function regularize.fixupCovalentGeom() will swap the angle, but
may cause large changes in other regions of the protein. If this is
the very beginning of a structure calculation this aspect should be
fine.
best regards--
Charles
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