[gmx-users] Making Disulfide Bonds

[James Starlight]

.. 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>

> 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>
>
>> 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>
>>
>>>  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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>
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