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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>:
> [EMAIL PROTECTED] 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
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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