[gmx-users] Hydrogen bonding

Andrew Horsfield horsfield at fecit.co.uk
Wed Jan 30 10:53:10 CET 2002


I am looking at the interaction of a small molecule with a protein. The
problem that concerns me is that interactions with other atoms in the
protein are pulling the small molecule away from the site suggested by
experiment, and I am trying to track down the root of this.

I suspect that hydrogen bonds are the key here. Gromacs gives only
moderate agreement with experiment for the length of the hydrogen bonds I
am interested in (distances are in Angstroms):

    Gromacs       Experiment
      3.11          2.75
      3.02          2.88

Is this what you would expect from a force field, or is it possible to get
better agreement?



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