[gmx-users] Making Disulfide Bonds

[Francesco Oteri]

Hi James,
usually I insert by hand a bond in the topology file between the two 
atoms and then I minimize.
This bond doesn't cause the generataion of angles and dihedrals, butit  
is enough to make the atom closer.

Francesco
Il 28/04/2012 16:08, James Starlight ha scritto:
> .. and the main question- what should be in mdp file of such 
> restrained minimisation ?
>
> Today I've done vry properly minimisation of such system in vacuum 
> with the CG minimisator and applied disres ( above example ) with big 
> force constant ( disres options have been defined in the minim.mdp 
> file ). As the result I have not noticed any perturbation in the 
> distance between two S-S atoms the distance between wich I've constrained.
>
>
>
> 2012/4/28 James Starlight <jmsstarlight at gmail.com 
> <mailto:jmsstarlight at gmail.com>>
>
>     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 <francesco.oteri at gmail.com
>     <mailto:francesco.oteri at gmail.com>>
>
>         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 <jmsstarlight at gmail.com
>         <mailto: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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