patch LINK - cyclizing a protein

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Thu Sep 25 2008 - 13:34:19 CDT

Hi all,

I am trying to cyclize a protein to run simulations on it. I tried the patch LINK command stating the residue numbers; the structure was cyclic, but the valencies weren't correct for the bonded atoms. So I was wondering:

1- would the order of specifying the residues matter?

2- can I use the patch LINK specifying the NTER and CTER? What would be the correct script for that?

3- There was also a suggestion to run the simulation with "constraint atoms"; I tired to search the archives on how to do that, but got no results.

Thanks
Rabab

      

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