[gmx-users] Making Disulfide Bonds

James Starlight jmsstarlight at gmail.com
Sat Apr 28 11:59:49 CEST 2012

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

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

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