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Hi,<br>
<br>
If it's the same protein you can extract the trajectories with the
coordinates of the protein only using trjconv.<br>
<br>
Ran.<br>
<br>
Afonso Duarte wrote:
<blockquote cite="mid434633.32244.qm@web60019.mail.yahoo.com"
type="cite">Hi to All,<br>
<br>
I have some simulations of the same protein in different solvents, with
different number of atoms for each (different solvent number of atoms).
<br>
I would like to calculate a rmsd matrix to compar the backbone of the
different sims.<br>
<br>
I have tried g_rms with the -f2 option to include the second
trajectory, however it finishes with a fatal error because teh number
of total atoms is different in both trajectories.<br>
<br>
Does anybody know how to solve this question? Is it possible to produce
the rmsd matrix in a different way?<br>
<br>
Thanks in advance<br>
<br>
Afonso<br>
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<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
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