[gmx-users] pdb as topology file
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 6 15:41:01 CEST 2004
On Tue, 2004-04-06 at 15:05, Lishan Yao wrote:
> My pdb file only has C-alpha and the trajectory file only has C-alpha
> too. You think this will cause any problem?
if you think that the pdb file matches the xtc, then you can try to do
trjconv -fit -o xxx.pdb
and see what it (xxx.pdb) looks like
> On Tue, 2004-04-06 at 07:57, David van der Spoel wrote:
> > 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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