Hello,<br> The molecule is not planar it is 3D. Also I would like to mention that the same reference structure gave me result earlier. I chose protein as group for least square fit and CA for RMSD calculation.<br>Thanks and regards,<br>
Nishtha <br><br><div class="gmail_quote">On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
<div class="Ih2E3d">nishtha pandey wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
Thank you for your response. It is a protein molecule containing 610 amino acid residues.<br>
</blockquote>
<br></div>
you didn't answer my question.<br>
please inspect the molecular structure at the time point where the error occurs.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks and regards,<br>
Nishtha<div class="Ih2E3d"><br>
<br>
On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
nishtha pandey wrote:<br>
<br>
Hello everyone,<br>
While trying to do the RMSD analysis of my<br>
trajectory file I am facing the error " Too many iterations in<br>
routine JACOBI". I have gone through the archives which suggests<br>
that such problem arises if there is mismatch between the<br>
reference structure and trajectory. However in my case the<br>
problem lies somewhere else because, using the same .tpr file<br>
and .trr file I have done RMSD analysis earlier also and it<br>
worked fine. The g_rms program is giving error but, for the<br>
same set of input files g_rmsdist is working fine.<br>
<br>
g_rmsdist doesn't use lsq fitting.<br>
<br>
Is you molecule linear or planar? (i.e. not 3D)?<br>
<br>
Kindly help.<br>
Regards,<br>
Nishtha<br>
<br>
<br>
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</div></blockquote><div><div></div><div class="Wj3C7c">
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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