[gmx-users] Making Disulfide Bonds

[Justin A. Lemkul]

On 4/28/12 10:08 AM, James Starlight wrote:
> .. 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.
>

You need to add the applicable distance restraint settings for them to be utilized.

http://manual.gromacs.org/online/mdp_opt.html#nmr

-Justin

>
>
> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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