Thanks Mark and Marzinek,<br><br>The Problem is solved:<br><br>g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx<br><br>> chain A<br><br>Found 1234 atoms with chain identifier A<br><br> 19 chA : 1234 atoms<br>
<br>> name 19 chainA<br><br><br>> chain B<br><br>Found 1234 atoms with chain identifier B<br><br> 20 chB : 1234 atoms<br><br>> name 20 chainB<br><br><br>> q<br><br><br><div class="gmail_quote">
2012/1/10 Marzinek, Jan <span dir="ltr"><<a href="mailto:j.marzinek10@imperial.ac.uk">j.marzinek10@imperial.ac.uk</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p>So as you can see Gromacs does not support multi file input :) Create one index file and specify there your two groups. Then g_hbond will ask you to choose two groups from this file.</p>
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<p>Jan</p>
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<div><font face="Arial">Jan Marzinek<br>
PhD Candidate<br>
Centre for Process Systems Engineering<br>
Department of Chemical Engineering<br>
Imperial College London<br>
South Kensington Campus<br>
London SW7 2AZ<br>
E: </font><a href="mailto:j.marzinek10@imperial.ac.uk" target="_blank"><font face="Arial">j.marzinek10@imperial.ac.uk</font></a><br>
<font face="Arial">M: <a href="tel:%2B44%280%297411%20640%20552" value="+447411640552" target="_blank">+44(0)7411 640 552</a></font></div>
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<div style="DIRECTION:ltr"><font color="#000000" face="Tahoma"><b>From:</b> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] on behalf of ahmet yıldırım [<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>]<br>
<b>Sent:</b> Tuesday, January 10, 2012 8:13 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] multi file input for index files<br>
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<div>Dear users,<br>
<br>
I created two different index files (A.ndx and B.ndx). <span lang="en">
<span>I want to run</span> <span>the two files</span> <span>
at the same time.<br>
e.g.<br>
g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx<br>
where, I want to calculate the hydrogen bonds between A and B.<br>
This command is giving the error as it expected. "</span></span>Gromacs tools do not support multi file input for index files" from
<a href="http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html" target="_blank">
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html</a>. Is this correct? If no, what should I do?<br>
<br>
Thanks in advance<br>
-- <br>
Ahmet Yıldırım<br>
<br>
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