<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Tsjerk,<br>The trjconv is not working, it is likely that i am not issuing the proper commands.<br><br><br>--- My ndx file - - -<br>Select group for output<br>Group 0 ( System) has 2619 elements<br>Group 1 ( Protein) has 2619 elements<br>Group 2 ( Protein-H) has 2619 elements<br>Group 3 ( C-alpha) has 873 elements<br>Group 4 ( Backbone) has 2619 elements<br>Group 5 ( MainChain) has 2619 elements<br>Group 6 (MainChain+Cb) has 2619 elements<br>Group 7 ( MainChain+H) has 2619
elements<br>Group 8 ( SideChain) has 0 elements<br>Group 9 ( SideChain-H) has 0 elements<br>Group 10 (r_1-152_r_457-595) has 873 elements<br>Group 11 (r_153-304_r_596-734) has 873 elements<br>Group 12 (r_305-456_r_735-873) has 873 elements<br>Group 13 ( a_1-456) has 456 elements<br>Group 14 (a_1-456_a_1369-1785) has 873 elements<br>Group 15 (a_457-912_a_1786-2202) has 873 elements<br>Group 16 (a_913-1368_a_2203-2619) has 873 elements<br>Group 17 (a_1-456_a_1369-1785_a_457-912_a_1786-2202_a_913-1368_a_2203-2619) has 2619 elements<br><br><br>Kindly advice<br>nahren<br><br>--- On <b>Mon, 5/10/10,
nahren manuel <i><meetnahren@yahoo.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: nahren manuel <meetnahren@yahoo.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, 3:50 PM<br><br><div id="yiv1815093403"><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">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">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;" 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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<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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