[gmx-users] ligand drifting
spoel at xray.bmc.uu.se
Tue Jul 13 21:23:01 CEST 2004
On Tue, 2004-07-13 at 18:38, A. A. Jeyaprakash wrote:
> Dear gromacs users,
> My ligand is drifting away from the binding-site of the protein
> during the dynamics. How one can avoid this situation? Is there a way to
> fix any one of the ligand atom?
Is it really or is it due to the pbc?
If it is real you can keep it there with distance restraint, but then
what will you get out? Maybe it is not a good binding site, or maybe the
forcefield does not describe your ligand well.
> Thanks in advance,
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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