[gmx-users] Ligand-protein interaction scoring

Douglas Houston douglas at davapc1.bioch.dundee.ac.uk
Wed Feb 18 00:35:01 CET 2004


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".
However, looking at the .gro output of mdrun, it appears that the
coordinates are slightly different from those in the input .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, or are there other ways of doing this in Gromacs that I'm

Thanks for any help,

Douglas R. Houston
University of Dundee,
MSI/WTB complex,
Dow Street,

Tel. +44 (0)1382 348354

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