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On 8/06/2012 12:34 PM, Malai wrote:
<blockquote
cite="mid:CANDSGMHGsHNs8U6rk1ZWD0MbYJhfSE14mcRdue61mnUTeJF3Aw@mail.gmail.com"
type="cite">Dear Mark, <br>
<br>
Thanks for mail. you mean I need to define in mdp file?.</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CANDSGMHGsHNs8U6rk1ZWD0MbYJhfSE14mcRdue61mnUTeJF3Aw@mail.gmail.com"
type="cite"> Can you please guide me how to do that. Thanks.<br>
</blockquote>
<br>
<a
href="http://www.gromacs.org/Documentation/File_Formats/Index_File">http://www.gromacs.org/Documentation/File_Formats/Index_File</a><br>
<br>
Mark<br>
<blockquote
cite="mid:CANDSGMHGsHNs8U6rk1ZWD0MbYJhfSE14mcRdue61mnUTeJF3Aw@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Fri, Jun 8, 2012 at 10:30 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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 class="HOEnZb">
<div class="h5">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 moz-do-not-send="true"
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
class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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</font></span></blockquote>
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