[gmx-users] procedure for creating an S-S bridge

[OZGE ENGIN]

Thank you Mark, but I am a little bit confused.

In the link you sent to me, http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is described in the specbond.dat file (in the first line). However, the following sentence is written under the given table: 

"To describe new possible special bonds, such as disulfides, so that pdb2gmx can generate them for you, you should add new lines similar to these example lines, and update the counter in the first line. "

So, I understood that the description made within the table does not describe the Cys-Cys bond. Then, what does it represent?  
After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH in the .gro file. 

So, which one is true?

Additionaly, I think, this type of information is not enough to create a disulphide bond. My cysteine residues are not directed to each other for making a Cys-Cys bond. So, what types of steps do I have to follow ? There are papers, of course, in which these types of bonds are made, but the description is not made properly. 

Thanks in advance




-----Original Message-----
From: "Mark Abraham" <mark.abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Mon, 3 Mar 2008 10:15:48 +1100 (EST)
Subject: Re: [gmx-users] procedure for creating an S-S bridge

> Hi all,
>
> I want to create an S-S bond within my peptide. So, I used the CYSH type
> cysteine residue and pdb2gmx with -ss option. However, I saw that the S-S
> bridge was formed between the ARG-CYS pair but not between the CYS-CYS
> pair.

That's not possible with the unmodified form of specbond.dat - you are
probably seeing a visualization artefact
http://wiki.gromacs.org/index.php/Trajectory_Visualisation#Topology_bonds_vs_Rendered_bonds.

> So, I think -ss option with pdb2gmx is not enough to make this bond. What
> additional steps do I follow to construct this bond ?

Check out http://wiki.gromacs.org/index.php/specbond.dat

Mark

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Ozge Engin
=================================
Computational Science & Engineering
Koc University