[gmx-users] pdb as topology file

[David van der Spoel]

On Tue, 2004-04-06 at 16:49, Lishan Yao wrote:
> Wait a second, then it should give me 10 times smaller number not 10
> times larger.In the covariance matrix analysis, gromacs gives me nm^2 as
> the unit. Most of my C-alpha only have motion about 0.5 angstroms. The
> biggest number I get from g_covar is about 1.6 nm^2. That is a big
> number. 
> 
> Lishan  
> 
> On Tue, 2004-04-06 at 09:48, Lishan Yao wrote:
> > 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. 
> > 
So your trajectory uses Angstrom. GROMACS scales the pdb but not the
traj. In that case you may want to scale the reference pdb using
editconf -scale.


> > Best,
> > Lishan
> > 
> > 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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> 
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-- 
David.
________________________________________________________________________
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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