Hi Nahren,<br><br>You probably used make_ndx for making the index file. Unfortunately it sorts the indices. You have to construct it in such a way that that the indices are in the order you want them. You can script the generation, based on the chain ID, or you can make separate index files that you concatenate together. In the latter case, do mind to remove the index group tags that are placed at the top of each file and add such a tag at the top of the concatenated file.<br>
<br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Tue, May 11, 2010 at 3:35 PM, nahren manuel <span dir="ltr"><<a href="mailto: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;" valign="top">
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><<a href="mailto:meetnahren@yahoo.com" target="_blank">meetnahren@yahoo.com</a>></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<br>From: nahren manuel <<a href="mailto:meetnahren@yahoo.com" target="_blank">meetnahren@yahoo.com</a>><div class="im"><br>Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ<br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
</div>Date: Monday, May 10, 2010, 3:50 PM<div><div></div><div class="h5"><br><br><div><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">
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><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></i></b> wrote:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>><br>Subject: Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Date: Monday, May 10, 2010, 3:35 PM<br><br><div>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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<br>post-doctoral researcher<br>Molecular Dynamics Group<br>Groningen Institute for Biomolecular Research and Biotechnology<br>University of Groningen<br>The Netherlands<br>