[gmx-users] rotacf error

[Mario Andres Rodriguez Pineda]

How I can remove the prolines, I have 6 in the protein...

Em dom., 15 de dez. de 2019 às 03:10, David van der Spoel <
spoel at xray.bmc.uu.se> escreveu:

> 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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-- 
*MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA*
*Estudiante Doctorado en Biotecnología*

*UNAL- MEDELLÍN/ IQ- USP*

*Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas *
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