[gmx-users] pca on amber MD output

[Tsjerk Wassenaar]

Hi Nadia,

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
file).

Cheers,

Tsjerk

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.
>
> Regards,
>
> Nadia
>
>
> 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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>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336