[gmx-users] pdb as topology file
yaolisha at msu.edu
Tue Apr 6 16:03:00 CEST 2004
It looks fine. It seems that gromacs uses nm as the coordinate unit. My
trajectory and pdb file (from amber) use angstrom as the unit.
On Tue, 2004-04-06 at 09:38, David van der Spoel wrote:
> 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
> > Lishan
> > 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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