[gmx-users] pdb as topology file

[Lishan Yao]

My pdb file only has C-alpha and the trajectory file only has C-alpha
too. You think this will cause any problem?

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
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.