[gmx-users] assign disulfide bond
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.
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