[gmx-users] pca on amber MD output
tsjerkw at gmail.com
Fri Oct 6 13:09:43 CEST 2006
Gromacs reads .pdb files (single or multimodel ones) perfectly. The
programmers have noted that .pdb files are in Angstroms usually.
Besides, you don't need an additional .pdb file when reading a .pdb
trajectory (if required you can give the same file as a structure
On 10/6/06, nadiav at soton.ac.uk <nadiav at soton.ac.uk> wrote:
> Hi Mark,
> Thank you very much for the clarification. I am also testing this at the
> moment running with and without Anstroms/nm conversions.
> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> > nadiav at soton.ac.uk wrote:
> > > Hi gromacs users,
> > >
> > > I am a new user to gromacs and realise that there are lots of comments
> > on
> > > the archive already about using gromacs with amber outputs but I am
> > getting
> > > rather mixed messages.
> > >
> > > I would like to clarify a few things. I have an Amber trjectory file
> > saved
> > > through VMD in a .pdb format and a pdb file for the topology.
> > >
> > > I see that some say that one should convert the trajectory file, some
> > say
> > > that gromacs reads .pdb and others mention changing the extension to
> > .g87
> > > and so on. My main question is about the fact that amber works in
> > > Angstroms and gromacs in nm. Should I convert my trajectory.pdb and
> > > topology.pdb to nm before carrying out principal component analysis?
> > There would be no need, since PCA is scale-independent. Further, the PDB
> > format prescribes the use of Angstroms, so I expect any software to
> > presume the use of Angstroms in any PDB file (since they can't tell the
> > point of origin of the PDB file). You could, of course, test this
> > yourself.
> > Mark
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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