How are you. I am trying to do refinement using the eefx and I need to add cis
bond between residue 40 and 41, proline is the 41st. In my script I have the
following
# load PDB to generate PSF
import glob
protocol.loadPDB( glob.glob(inTemplate)[0],
deleteUnknownAtoms=True, )
import psfGen
psfGen.cisPeptide(resid=40)
while the calculation ran, in some of the structure I am missing atoms between
the 40th and 41st residues. Also even in the structures that did not have
missing atoms, it seemed the protons on the 40th glycine are linked together. I
would appreciate any help. Thank you so much.
Best,
Adel
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