From: Narang, Pooja, Ph.D. (Narang.Pooja_at_mayo.edu)
Date: Fri Jun 27 2008 - 15:24:38 CDT
I am trying to make a cyclic peptide. I have used patch link command to link the N and C terminals as given below:
patch LINK U:1 U:5
Now, as I visulaize the structure in VMD, the dihedral angle omega of the new peptide bond is not ~180 degree, rather it is ~130 degree, and after minimization and equlibration this dihedral becomes even more distorted (~30-50 degree).
Is there a way to make an actual peptide bond between two amino acids to make cyclic peptide. Or do I have to constraint this dihedral for my simulation?
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