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.
Francesco 2012/4/28 James Starlight <[email protected]> > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco
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