[gmx-users] calculate torsional energy of the ligand from the trajectory

David spoel at xray.bmc.uu.se
Tue May 3 17:03:02 CEST 2005

On Tue, 2005-05-03 at 16:42 +0200, Minami Mo wrote:
> Hi all,
> Does anyone know how to extract the torsional energy of (only) the
> ligand from the MD simulation bounded to a protein? I have been
> searching for it for some times but seem it was not asked before.
> My current idea is to extract the ligand in each frame to a pdb file,
> and do the calculation. Any suggestion or tool that may serve this
> purpose?
You can use mdrun -rerun in which you use a topology where all the
protein dihedrals are taken away.

> Thanks.
> Minami
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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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