[gmx-users] Making Disulfide Bonds

francesco oteri francesco.oteri at gmail.com
Sat Apr 28 12:04:37 CEST 2012

Hi James,
usually people run a minimization using distance restrain on the two atoms
in order to
make them closer.
Then the obtained cnfiguration is used to recalculate the topology.


2012/4/28 James Starlight <jmsstarlight at gmail.com>

> Dear Gromacs Users!
> I have a model of my protein wich has 4 S-S bounds in the loop regions. So
> I want to define in topology all those four S-S linkage.
> Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also
> I've tried to check this bond in pymol and found that distance between that
> two Cys Cys are larger for S-S occurence) due to some inaccyracy of model.
> Is there any way to define such missing S-S manually? On the gromacs site
> I've found possible sollution by means of spechbond.dat editing. I've tried
> to increase distance between S-S atoms but this have not had desirebly
> affect.
> In the topology.top file I've found that the S-S bonds beetween S atoms
> are defined in the bond section without any type for such bond type. Also
> I've found that the same enties are present in the angle and dihedralls
> sections.  Could I define the same contact only in the bond section and
> further minimise my system to obtain new S-S linckage or should I also
> define all other enties ( like dihedralls etc) for that bond ?
> Thanks for help
> James
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Cordiali saluti, Dr.Oteri Francesco
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