Re: Problem in making cyclic peptide

From: Peter Freddolino (
Date: Fri Jun 27 2008 - 16:11:21 CDT

Hi Pooja,
psfgen will not change the coordinates when you add a bond, so what you
should probably do is apply a constraint to this dihedral while
minimizing to make sure you fall into the trans well. Once this is done
you should be fine. This is an "actual" peptide bond, but psfgen won't
force the coordinates to match what you expect on its own.

Narang, Pooja, Ph.D. wrote:
> 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

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