[gmx-users] Making Disulfide Bonds
jmsstarlight at gmail.com
Sat Apr 28 12:51:34 CEST 2012
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 ?
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.
> 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
>> 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
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> Cordiali saluti, Dr.Oteri Francesco
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