Re: Problem in making cyclic peptide

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jun 27 2008 - 16:01:27 CDT

After you apply the patch in your psfgen script, try adding the
following line:

regenerate angles dihedrals

This is generally a good idea after any patches since angles and
dihedrals are normally only generated when building segments.
Hopefully that will do the trick.

On Jun 27, 2008, at 3:24 PM, 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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