[gmx-users] Ligand-protein interaction scoring

Michael Brunsteiner mbx0009 at yahoo.com
Wed Feb 18 10:09:01 CET 2004

--- Douglas Houston <douglas at davapc1.bioch.dundee.ac.uk> wrote:
> Hi,
> I am intending to use Gromacs to "score" various ligand-protein
> complexes.
> So far to do this I have been using mdrun with nstep=0, followed by
> g_lie.
> I was assuming that with no MD/minimization, this should be able to
> gauge
> the interaction energy between the ligand and the protein "as-is".

if you generated the original complexes with another program
(some docking software) you should minimize the energy of each complex
in gromacs before considering the calculated energies.
This is crucial because small differences in repulsive parameters
may give you BIG differences in the energy.

> However, looking at the .gro output of mdrun, it appears that the
> coordinates are slightly different from those in the input

what is slightly ? If you talk about changes somewhere in
the range of 0.001 Angstrom or smaller this is normal and due
to the finite precision/rounding errors ... should
not worry you.

> .gro file. Is
> this machine error, or do I need to use a different keyword to
> prevent
> mdrun from doing any MD/EM? Is this even a reasonable way of going
> about this,

unless you fit your LIE parameters (alpha, beta) to reproduce
experimental results obtained for your specific protein
(or something VERY similar) and then calculate AVERAGE interaction
energies via, albeit short, MD runs (instead of single point energies)
you will only get a VERY rough estimate for the ranking of your 

> or are there other ways of doing this in Gromacs that I'm
> overlooking?
> Thanks for any help,
> Douglas R. Houston
> University of Dundee,
> MSI/WTB complex,
> Dow Street,
> Dundee,
> UK,
> DD1 5EH
> Tel. +44 (0)1382 348354
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