VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 13 2009 - 01:20:11 CDT

What happened is that you did not build your system with them to begin with.
Disulfide bonds require using the patch "PRES DISU" (I think) when building
your psf, e.g., through the "add patch" box in autopsf. Usage of the patch
command can be found in the psfgen manual as well as in the standard charmm
topology file containing it.

 

However, they will not break once they are there. As they are covalent
bonds anyway, if you were hypothetically able to raise the temperature
enough to break them, you would have much bigger problems with your protein!

 

 

From: Andres Morales N [mailto:andresmoralesn2_at_hotmail.com]
Sent: Tuesday, October 13, 2009 1:14 AM
To: gumbart_at_ks.uiuc.edu
Subject: RE: vmd-l: Disulfude bonds

 

During the simulation the protein unfold, so distances between sulfures of
Cysteins are too big (12-15 A) , so I think someting happened with disulfide
bonds.

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From: gumbart_at_ks.uiuc.edu
To: andresmoralesn2_at_hotmail.com; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Disulfude bonds
Date: Tue, 13 Oct 2009 01:08:13 -0500

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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