[gmx-users] assign disulfide bond

HongTham hongtham0709 at gmail.com
Fri Apr 24 10:55:05 CEST 2015

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.
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?

Thank you so much.


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