Hi Nahren,<br><br>You can do that using trjconv and an index file with the atom indices as they are in the order as they have to be.<br><br>But is that really your problem? To understand what happened, it would help if you gave the series of commands that led to these results.<br>
<br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Mon, May 10, 2010 at 11:42 AM, nahren manuel <span dir="ltr"><<a href="mailto:meetnahren@yahoo.com">meetnahren@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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<p style="margin-bottom: 0in;">Dear Gromacs Users,<br><br>I simulated
two homologous (proteins) , and noticed after the simulation that in
one trajectory, the protein is stored as ABCXYZ and in another it is
as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ
is another trimer, so the system is a trimer-trimer complex)</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">I should not have any issues for most
of my trajectory analysis. But when I wanted to get a correlation
plots of the CA-CA from the covariance matrix, the plots cannot be
compared, as the information in the trajectory is different.</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">So is there a way that I can convert my
trajectory from ABCXYZ to AXBYCZ.
</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">Thank you,</p>
<p style="margin-bottom: 0in;">nahren</p>
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<br>--<br>
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<br>post-doctoral researcher<br>Molecular Dynamics Group<br>Groningen Institute for Biomolecular Research and Biotechnology<br>University of Groningen<br>The Netherlands<br>