[gmx-users] Disulphide bonds

Alan Dodd anoddlad at yahoo.com
Mon Jul 31 15:08:44 CEST 2006

I use the option -merge with my SS-linked peptides,
and pdb2gmx always asks me if I want to join my
cysteines with a bond.  If they're internal to the
protein, perhaps it's either that they're too far
apart, or you need -ignh as otherwise they've got
hydrogens on and potentially can't bond.

--- Cesar Araujo <cesar.araujo at oulu.fi> 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???
> Regards,
> César.-
> Cesar Araujo, Lic. of Chemistry
> Department of Molecular Endocrynology
> Oulu University Hospital
> phone: +358 8 3155632
> e-mail: cesar.araujo at oulu.fi
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