VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 13 2009 - 01:08:13 CDT

Assuming you built your system correctly, the disulfide bonds are covalent,
meaning that no matter what, they will not be broken in your simulation.
You should be able to confirm this by looking at your trajectory in VMD.

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Andres Morales N
Sent: Tuesday, October 13, 2009 1:01 AM
To: VMD
Subject: vmd-l: Disulfude bonds

 

Dear VMD users:

I am studing conformations of a protein that has three disulfude bonds in
its native state, I equilibrate the system (protein plus explicit water) at
1000 K during 10 ns using molecular dynamic simulation with NAMD. Now I
want to analize structures that were produced during the simulation. I need
to identify if disulfude bonds have been broken o not. Does anybody know how
can I do that? Are there any script to do it?

Thanks for your suggestion

Andres

  _____

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