Gromacs

Making Disulfide Bonds

    Table of contents
    No headers

    Version as of 07:42, 2 Dec 2021

    to this version.

    Return to Version archive.

    View current version

    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?