[gmx-users] ELNEDIN disulfide bridge
x.periole at rug.nl
Mon May 10 16:21:23 CEST 2010
There no specific term associated with di-sulfide bridge in ElNeDyn.
however recommended to use a cutoff for the Elastic network of 0.9 nm.
The two Backbone beads are certainly within that distance so it is
Nevertheless to include the disulfide bridge explicitly you should add a
bond in your topology between the two side chain beads. The same force
constant as in regular Martini should be used. The changes between
Martini relate to other things.
On May 10, 2010, at 4:03 PM, Lea Thøgersen wrote:
> I am trying to set up an ELNEDIN simulation of a protein which
> contain a disulfide bridge. As all the bonded interactions are
> changed compared to the MARTINI force field, I do not know how the
> parameters should be set for this bond, as it would seem
> unreasonable simply to use the MARTINI values.
> Has anyone reparameterised the disulfide bond for the ELNEDIN model,
> or have an idea of how I should proceed?
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