Problem in making cyclic peptide

From: Narang, Pooja, Ph.D. (Narang.Pooja_at_mayo.edu)
Date: Fri Jun 27 2008 - 15:24:38 CDT

• Next message: Gianluca Interlandi: "carbohydrates: CHARMM versus AMBER"
• Previous message: Peter Freddolino: "Re: Problem in making cyclic peptide"
• Next in thread: JC Gumbart: "Re: Problem in making cyclic peptide"
• Reply: JC Gumbart: "Re: Problem in making cyclic peptide"
• Reply: Peter Freddolino: "Re: Problem in making cyclic peptide"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi all,
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?

Thanks
Pooja

• Next message: Gianluca Interlandi: "carbohydrates: CHARMM versus AMBER"
• Previous message: Peter Freddolino: "Re: Problem in making cyclic peptide"
• Next in thread: JC Gumbart: "Re: Problem in making cyclic peptide"
• Reply: JC Gumbart: "Re: Problem in making cyclic peptide"
• Reply: Peter Freddolino: "Re: Problem in making cyclic peptide"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Mon Oct 13 2008 - 12:18:18 CDT