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 < sp...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.