Making Disulfide Bonds

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    The easiest way to do this is by using the mechanism implemented with the specbond.dat file and pdb2gmx. This requires that the two sulfur atoms be within a distance + tolerance (usually 10%) in order to be recognised as a disulfide. If your sulfur atoms are not this close, then either you can

    • edit the contents of specbond.dat to allow the bond formation and do energy minimization very carefully to allow the bond to relax to a sensible length, or
    • run a preliminary EM or MD with a distance restraint (and no disulfide bond) between these sulfur atoms with a large force constant so that they approach within the existing specbond.dat range to provide a suitable coordinate file for a second invocation of pdb2gmx.

    Otherwise, editing your

    .top file

    by hand is the only option

    Page last modified 01:26, 10 Oct 2009 by JLemkul?