[gmx-users] problem with g_rmsf

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 13 13:32:09 CET 2006

Hi Adriana,

I have to clarify a bit (and admit I was slightly wrong). The option -q is
an input .pdb file to which the rmsf values can be added, which are then
together output to the file given by the -oq option. When using the -oq
option without -q the reference structure (from -s) will be used for that.
If you only supply a -q... I think it is ignored. There is no way to make
the comparison for you. You can use g_rmsf to calculate the root mean square
fluctuation, the B-factor (-ox) or the anisotropic temperature factors. But
you'll have to do the comparison yourself.



On 2/13/06, Adriana Pietropaolo <adriana at ms.fci.unibo.it> wrote:
> On Mon, 13 Feb 2006, X.Periole wrote:
> >
> > I am affraid that Tsjerk is right. -q is an option for
> > output. There is a mistake in the manual ...
> >
> > XAvier
> >
> ....
> ok...
> and so to compare a pdb from NMR and my trj I have to do a tpr concerning
> this pdb, related to the option -s?
> thanks...
> Adriana
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Tsjerk A. Wassenaar, M.Sc.
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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