Thanks! trjconv with -s works fine!<br><br>
<div class="gmail_quote">2009/1/19 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>Hi,<br><br>Are the two chains in a single molecule definition or in two molecule definitions?<br><br>There are no chain identifiers written in the tpr file.<br>But mdrun of Gromacs 4.0 will automatically generate chain identifiers for each molecule.<br>
In Gromacs 3 no chain identifiers will be written.<br><br>You can always run trjconv with for -s a pdb file with chain identifiers<br>and they will be copied to the pdb output.<br><br>Berk<br><br>
<hr>
Date: Mon, 19 Jan 2009 16:45:50 +0800<br>From: <a href="mailto:nomadoro@gmail.com" target="_blank">nomadoro@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>Subject: [gmx-users] mdrun output conformation file loses chain identifier
<div>
<div></div>
<div class="Wj3C7c"><br><br>
<div>Hello!</div>
<div>I'm using GROMACS to perform a double-chain MD simulation. It surprises me that the mdrun output conformation file ( specified by -c ) contains no more chain identifier ( A or B ) that exists in the original input PDB file. So can someone tell me how to re-integrate the chain identifier into the output conformation file? <br clear="all">
<br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br></div><br></div></div>
<div class="WgoR0d">
<hr>
Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a></div></div><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>Sun Li<br>Department of Physics<br>Nanjing University, China<br>