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

[OZGE ENGIN]

So, from the explanation made within table I understood that after selecting -ss option, I would see the type of cys as CYS2 in the constructed .gro file as well as in the .top file since the CYS2 name appears in the 8 th and 9 th columns and they are described as the new name for residue A and residue B.

So, I should perform a preliminary simulation in order to make the corresponding cysteine residue within the cutoff?

-----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 20:46:15 +1100 (EST)
Subject: Re: Re: [gmx-users] procedure for creating an S-S bridge

> 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?

What do you think the second line of the file describes?

> After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH
> in the .gro file.

... and the pdb2gmx output doesn't report making a special bond, and using
pdb2gmx without the -ss option produces the same output. Your conclusion
here is...?

> 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.

See the final line of the specbond.dat page. You'll need to change your
input structure. Think about distance restraints and a preparatory MD
simulation.

Mark

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