Hi,<br> Thank you for your response. It is a protein molecule containing 610 amino acid residues. <br>Thanks and regards,<br>Nishtha<br><br><div class="gmail_quote">On Sat, Jan 24, 2009 at 4:37 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;">
Hello everyone,<br>
While trying to do the RMSD analysis of my trajectory file I am facing the error " Too many iterations in routine JACOBI". I have gone through the archives which suggests that such problem arises if there is mismatch between the reference structure and trajectory. However in my case the problem lies somewhere else because, using the same .tpr file and .trr file I have done RMSD analysis earlier also and it worked fine. The g_rms program is giving error but, for the same set of input files g_rmsdist is working fine.<br>
</blockquote></div>
g_rmsdist doesn't use lsq fitting.<br>
<br>
Is you molecule linear or planar? (i.e. not 3D)?<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Kindly help.<br>
Regards,<br>
Nishtha<br>
<br>
<br>
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David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
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