Re: What is LINK Patch?

From: Jian Liu (
Date: Mon Dec 07 2009 - 23:42:48 CST

Hello Myunggi
The LINK patch is used to link two end-point residue with a peptide bond, by deleting the H(N) in N terminal and the OH in C terminal and adding a BOND and some ANGLEs etc.
This is useful in joining two peptide chains or ringing a peptide chain.

I don't think LINK is a good choose for you.
Why not have a try of fix or constrain the alpha C atom in protein

Jian Liu
Master-degree graduate candidate majoring in Molecular Modelling
Department of Physical Chemistry & Chemical Physics
College of Chemistry, Chemical Engineering and Materials Science
Soochow University
Suzhou 215123, China

> From: Myunggi Yi <>
> To:
> Subject: namd-l: What is LINK Patch?
> Date: 2009-12-8 03:47:20
> Dear Namd users,

> I'd like to run simulations with a homo-tetrameric prtein (four subunits are not covalently bonded).
> Each subunit starts with SER and ends with GLY resiues.
> During the constant pressure equilibration, the distances between subunits will be scaled down, but
> I want to keep the distances between the subunits. (position restraints (the target structure's positions) will be scaled too, won't they?)
> I want to keep the whole protein as one image too.
> So, I want to deal these four peptides as one segment or unit,
> but I don't know how to.
> What does LINK patch do?
> Can I achieve my goals with this patch? (image is not critical)
> How can I used this patch?
> --
> Best wishes,
> Myunggi Yi
> ==================================
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