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

Mark Abraham mark.abraham at anu.edu.au
Mon Mar 3 10:46:15 CET 2008

> 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


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