[gmx-users] rotacf error

[David van der Spoel]

Den 2019-12-15 kl. 04:13, skrev Mario Andres Rodriguez Pineda:
> Hi all
> I want to calculate the order parameter of the NH vector for each  amino
> acids of a protein  in a gromacs trajectory for compare with NMR
> experimental data.
> I found that it can be calculated using rotacf to calculate the correlation
> time, when trying to run the program I get an error. In the attached file I
> show more details about the error andhow I created the index. Could you
> help me to correct the index for calculate the correlation time and in turn
> the order parameter S2?
> Thanks for your help.
> 
> 
you likely have Proline residues in your protein which do not have a H. 
More tricky, if you have two prolines you get an even number of atoms 
again but it can be completely wrong. Solution is to remove prolines in 
make_ndx before you select a group of NH.

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se