[gmx-users] assign disulfide bond

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 27 12:43:53 CEST 2015

On Fri, Apr 24, 2015 at 1:38 PM, Mark Abraham <mark.j.abraham at gmail.com>

> 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.


Please leave discussion on the list, so others can learn and contribute. :-)

Off-list, HongTham said:

> I understand you mean. I am just a new one in Gromacs so I feel litte
Follow you, I need to run a short md simulation with distance constraint
between to two Cystein residues. I saw a instruction about the disrc_fc
applied in mdp file. And then, when two these residues come closed enough
to make disufide bond, I dont know what i have to do next. Do I have to
generate again the top file for that structure? I thought the top file just
is generated one time when I run pdb2gmx command for initial structure and
we need new top file for new structure with have this disulfide.

A normal workflow doesn't change the topology, but yours needs to modify
the conformation to permit the topology you actually want to be able to be
generated. The "extra" topology is the one you are using to clean up the
initial conformation.


> Mark
> Thank you so much.
>> Hongtham
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