<br>Hi Adriana,<br><br>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.
<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 2/13/06, <b class="gmail_sendername">Adriana Pietropaolo</b> <<a href="mailto:adriana@ms.fci.unibo.it">adriana@ms.fci.unibo.it</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">On Mon, 13 Feb 2006, X.Periole wrote:<br><br>><br>> I am affraid that Tsjerk is right. -q is an option for
<br>> output. There is a mistake in the manual ...<br>><br>> XAvier<br>><br>....<br>ok...<br>and so to compare a pdb from NMR and my trj I have to do a tpr concerning<br>this pdb, related to the option -s?<br>
thanks...<br>Adriana<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>