[gmx-users] Disulphide bonds

Cesar Araujo cesar.araujo at oulu.fi
Tue Aug 1 12:47:36 CEST 2006

Cesar Araujo wrote:
> Hi,
> Anybody knows if there is some way to tell pdb2gmx to
> recognize automatically S-S bonds and not through the modification of
> specbond.dat file and -ss option???

it does if they are within the normal distance. are your pdb files ok?

I want to force some disulphide bond and simulate the structure to compare 
both (with and without the S-S bond). I was wondering if GROMACS can use 
SSBOND in pdb files directly. I'm writing some scripts using Expect language 
but at the moment I'm stucked with some TCL stuff.


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