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Dear Dr. Schwieters,
Thank you for your suggestions.
I am writing to request advice on how best to
patch unusual chemical moieties to the termini of peptide sequences. For
simplicity, I would like to define the moiety as a special type of amino acid
and then
use a toph.pep file to generate the sequence.-Russell
Hello Russell--
Are genCircPep.py or genModCircPep.py in the eginput/PSF_generation
subdirectory of the Xplor-NIH distribution useful in this regard? If
not, I can probably dig up some other examples.
best regards--
Charles
I have been able to move forward and construct a few cyclic beta peptide
foldamers (like ACPC-8) that
have qualitatively correct geometries. As I attempt to finish up, I have run
across two problems that might be of general interest.
Firstly, I receive interatomic distance and angle error messages when
running a sa_accept.inp script on the SA geometries. I believe this is because
the carbon and hydrogen atoms in each building block are
confined to a 5-membered ring. I have used only “CT” type carbons in the
building
blocks. Is it best to use another carbon type (such as “CP”) in the ring to
minimize
these errors or are the errors just an artefact and the final SA geometries
the same regardless of carbon type?
Also, I enforce a trans geometry between the HA/HB atoms of
each building block by defining an improper dihedral --HA CA CB HB-- that I
set to a value derived from the X-ray structure. I am very sceptical about
this! This improper may be the source of the problems above. Can anyone
suggest a better way to maintain a trans geometry
between the HA/HB and NH/CO moieties in cyclic beta peptides such as ACPC?
Any comments would be greatly appreciated
Thanks and best regards,
Russell
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