Dear MARK,<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000"><div class="im"><blockquote type="cite">Dear Mark, <br>
<br>
Thanks for mail. you mean I need to define in mdp file?.</blockquote>
<br></div>
No. Using one of the two ways I suggested earlier depend what you're
actually trying to do, but since your intention in using the CA
group is unknown to us, you're preventing yourself getting specific
help.</div></blockquote><div><br>The error is CA index file. So my intention is to use CA group and avoid the error. please suggest me how to use grompp or make CA index file for grompp in position restrained step. <br>
</div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000"><div class="im"><br>
<br>
<blockquote type="cite"> Can you please guide me how to do that. Thanks.<br>
</blockquote>
<br>
</div><a href="http://www.gromacs.org/Documentation/File_Formats/Index_File" target="_blank">http://www.gromacs.org/Documentation/File_Formats/Index_File</a><span class="HOEnZb"><font color="#888888"><br></font></span></div>
</blockquote><div><br>so i need to make index files for CA atoms of protein using make_ndx for CA. can you please explain how to make index file for CA using make_ndx.<br><br>Thanks for help. <br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><span class="HOEnZb"><font color="#888888">
<br>
Mark</font></span><div><div class="h5"><br>
<blockquote type="cite"><br>
<div class="gmail_quote">On Fri, Jun 8, 2012 at 10:30 AM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>On 8/06/2012 12:23 PM, Malai wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
After Successfully neutralizing and sd minimization of
the system, I got the below error when I try the grompp
for position restrained step. The command I used is
:grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o
complx_eqn1.tpr<br>
<br>
Any help will be highly appreciated.<br>
<br>
Many thanks.<br>
<br>
<br>
Error message:<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.5.5<br>
Source code file: readir.c, line: 1320<br>
<br>
Fatal error:<br>
Group CA not found in index file.<br>
Group names must match either [moleculetype] names<br>
or custom index group names,in which case you<br>
must supply an index file to the '-n' option of grompp.<br>
For more information and tips for troubleshooting,
please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
</blockquote>
<br>
</div>
</div>
Your .mdp file referred to a group for which grompp could find
no definition. Choose a better group or make a definition.<span><font color="#888888"><br>
<br>
Mark<br>
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</font></span></blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
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