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
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