[gmx-users] about complex MD

David spoel at xray.bmc.uu.se
Mon May 16 08:28:41 CEST 2005

On Mon, 2005-05-16 at 09:37 +0700, Natapol Pornputtapong wrote:
> Now I work on protein-ligand complex by GROMACS. The system that I
> prepare,has a ligand on outer of cell. When I run dynamics the ligand
> cannot soak in to the water and don't react with protein molecule. This
> is the first problem.
> >From past, I change the ligand coordinate to put the ligand into waters
> but when I run dynamics on this system the ligand is kicked from the
> system. What can I do for these problems. Please suggest me.

Please give more detail. If you have a structure for a complex it will
most likely stay together. Maybe you just have a PBC effect. Try
editconf -center and center on the protein.

> Thank you very much
> Natapol Pornputtapong
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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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