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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