[gmx-users] Making Disulfide Bonds

[James Starlight]

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
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120428/74344467/attachment.html>