[gmx-users] pdb as topology file

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 6 13:59:01 CEST 2004

On Tue, 2004-04-06 at 00:18, Lishan Yao wrote:
> Hi:
>    I use g_rms to calculate rmsd between a trajectory and a crystal
> structure, by taking the pdb file as the topology file. But
> unfortunately, g_rms gives me much lager numbers than what they should
> be. What could be wrong?
your pdb file may not have the sam enumber of atoms, e.g. H missing.
Then the indexing of e.g. C-alpha atoms will be wrong.
> Best,
> Lishan
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David van der Spoel, PhD, Assist. 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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