<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Tsjerk,<br><br>No the problem was not with GROMACS. I have one structure as a X-ray and the other i created by homology modeling based on this structure. So the difference arose because my starting structures themselves were different.<br><br>I did try trjconv with an index file , but it did not work out fine. I will check them once again before getting back.<br><br>Thank you<br><br>nahren<br><br>--- On <b>Mon, 5/10/10, Tsjerk Wassenaar <i><tsjerkw@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Tsjerk Wassenaar <tsjerkw@gmail.com><br>Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Monday, May 10, 2010, 3:35 PM<br><br><div id="yiv1498452246">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 rel="nofollow" ymailto="mailto:meetnahren@yahoo.com" target="_blank" href="/mc/compose?to=meetnahren@yahoo.com">meetnahren@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit; -x-system-font: none;" valign="top">
<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>
</td></tr></tbody></table><br>
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Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>
<br>post-doctoral researcher<br>Molecular Dynamics Group<br>Groningen Institute for Biomolecular Research and Biotechnology<br>University of Groningen<br>The Netherlands<br>
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