Hello,
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.
Thanks and regards,
Nishtha
On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel
<[email protected]>wrote:
> 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.
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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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