nishtha pandey wrote:
Hi,
Thank you for your response. It is a protein molecule containing 610
amino acid residues.
you didn't answer my question.
please inspect the molecular structure at the time point where the error
occurs.
Thanks and regards,
Nishtha
On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel
<[email protected] <mailto:[email protected]>> wrote:
nishtha pandey wrote:
Hello everyone,
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.
g_rmsdist doesn't use lsq fitting.
Is you molecule linear or planar? (i.e. not 3D)?
Kindly help.
Regards,
Nishtha
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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