From: Jian Liu (bay__gulf618_at_sina.com)
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
http://groups.google.com/group/bay__gulf618?hl=zh-CN
> From: Myunggi Yi <myunggi_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> 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
> ==================================
>
> 91 Chieftan Way
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: +1-850-645-1334
>
> http://sites.google.com/site/myunggi/
> http://people.sc.fsu.edu/~myunggi/
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:34 CST