[gmx-users] assign disulfide bond

Mark Abraham mark.j.abraham at gmail.com
Fri Apr 24 13:39:00 CEST 2015

On Fri, Apr 24, 2015 at 10:55 AM, HongTham <hongtham0709 at gmail.com> wrote:

> Hi all gmx user,
> I want to ask if there is the way to specialized the residue index to
> assign a disulfide bond between 2 apart Cysteins.

That wouldn't help you, because the resulting distance would be
non-physical, so you'd have crazy forces, etc.

> Because my protein is homology model so initial structure, 2 residues are
> apart each other. as the result, when I run pdb2gmx command, this disulfide
> bond can not be formed. (there is formed disulfide bond between 2 this
> Cysteins in wild type protein). I also took a look on specbond.dat  but
> there no residue index is specialized. There is only the description about
> the residue names and atom names.
> CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
> Could anybody help me?

In such cases, you should explore using distance restraints to pull the
relevant atoms close enough that the distance heuristic in pdb2gmx will
work for generating a topology with the disulfide bond next time.


Thank you so much.
> Hongtham
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