[gmx-users] PCA in dihdral space

Gleb Novikov blue.bossa87 at yahoo.com
Tue Aug 1 10:58:00 CEST 2017

 Dear Gromacs users!

In the tutorial I found that tomake a list for dihedral angles via mk_angndxI need to provide tpr file as an input.  
 Here some of my questions:
1)Is itpossible to make a list from pdb file (or convert pdb to tpr),assuming that my trajectory has been calculated not in Gromacs ?

2) Does this method good forcalculation of PCA of Chi-1 angle of the side chains (e.g to clarifythe contribution of the concerned rotation of the side-chain)?
Thanks !


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