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 <[email protected]
<mailto:[email protected]>>
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]
<mailto:[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]
<mailto:[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
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Cordiali saluti, Dr.Oteri Francesco
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