[gmx-users] Reorienting trajectories before PCA

[Chng Choon Peng]

Dear all,

   Thanks to Wei Fu and Bert for responding.
Oh yes, I never realized that I can use .gro or .pdb files with "-s" :)

Regards,
Choon-Peng

On 2/6/04 4:02 PM, "Bert de Groot" <bgroot at gwdg.de> wrote:

> Chng Choon Peng wrote:
>> 
>> Dear users,
>> 
>>     We need to reorient and combine 2 sets of 5ns trajectories before doing
>> a PCA using g_covar. We wish to show the differences on the same PC1 vs PC2
>> plot.
>> 
>> However, though I'm successful in extracting out the C-alpha trajectories
>> using trjconv followed by concatenating the 2 Ca trajectories using trjcat,
>> I'm not able to create an appropriate CA tpr file for g_covar to use.
>> 
>> Gromacs provide another tool called tpbconv that is supposed to give a pure
>> Ca tpx file but this option does not seem functional at this time.
>> 
>> Can anyone help? Thanks!
>> 
> 
> use a .gro or .pdb for the -s option of g_covar instead of .tpr
> 
> --
> 
> Bert
> 
> ATTENTION: Please note new phone/fax numbers below!
> 
> ____________________________________________________________________________
> Dr. Bert de Groot
> 
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11 
> 37077 Goettingen, Germany
> 
> tel: +49-551-2012308, fax: +49-551-2012302
> 
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/073
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