Hi Francesco! So I must define in the current topology the disres bettwen two S atoms ( in the below example 1 and 10 ) to apply hormonic restains
[ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 1 10 1 0 1 0.18 0.20 0.22 1.0 to restrain this atoms within 0.2 nm. Does it correct ? Or should I use some other disres for such task ? James 2012/4/28 francesco oteri <[email protected]> > 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 > > -- > 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 >
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