Re: [gmx-users] rotacf error
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.
Re: [gmx-users] rotacf error
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.
[gmx-users] rotacf error
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. -- *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* gmx_mpi make_ndx -f protein_md.tpr -o nh.ndx << EOF > a N | a H > r 590 | r 645 | r 649 | r 655 | r 664 | r 680 > 10 & !11 > name 12 NH > del 0-11 > q > EOF > name 12 NH > del 0-11 > q > EOF Reading structure file Reading file cbd212_md.tpr, VERSION 2018.6 (single precision) Reading file cbd212_md.tpr, VERSION 2018.6 (single precision) Going to read 0 old index file(s) Analysing residue names: There are: 146Protein residues There are: 23993 Water residues There are: 196Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 74517 atoms 1 Protein : 2342 atoms 2 Protein-H : 1186 atoms 3 C-alpha : 146 atoms 4 Backbone: 438 atoms 5 MainChain : 585 atoms 6 MainChain+Cb: 723 atoms 7 MainChain+H : 727 atoms 8 SideChain : 1615 atoms 9 SideChain-H : 601 atoms 10 Prot-Masses : 2342 atoms 11 non-Protein : 72175 atoms 12 Water : 71979 atoms 13 SOL : 71979 atoms 14 non-Water : 2538 atoms 15 Ion : 196 atoms 16 NA : 103 atoms 17 CL :93 atoms 18 Water_and_ions : 72175 atoms nr : group '!': not 'name' nr name 'splitch' nrEnter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > Found 146 atoms with name N Found 139 atoms with name H Merged two groups with OR: 146 139 -> 285 19 N_H : 285 atoms > Merged two groups with OR: 14 14 -> 28 Merged two groups with OR: 28 14 -> 42 Merged two groups with OR: 42 14 -> 56 Merged two groups with OR: 56 14 -> 70 Merged two groups with OR: 70 14 -> 84 20 r_590_r_645_r_649_r_655_r_664_r_680:84 atoms > Copied index group 10 'Prot-Masses' Copied index group 11 'non-Protein' Complemented group: 2342 atoms Merged two groups with AND: 2342 2342 -> 2342 21 Prot-Masses_&_!non-Protein: 2342 atoms > > Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'non-Protein' > gmx_mpi rotacf -s protein_md.tpr -f protein_nopbc.xtc -P 2 -d -n nh.ndx -o protein_rotacf.xvg -dt 1000 Group 0 ( NH) has 71979 elements Group 1 (SOL) has 71979 elements Group 2 ( non-Water) has 2538 elements Group 3 (Ion) has 196 elements Group 4 ( NA) has 103 elements Group 5 ( CL) has93 elements Group 6 ( Water_and_ions) has 72175 elements Group 7 (N_H) has 285 elements Group 8 (r_590_r_645_r_649_r_655_r_664_r_680) has84 elements Group 9 (Prot-Masses_&_!non-Protein) has 2342 elements Select a group: 7 Selected 7: 'N_H' --- Program: gmx rotacf, version 2018.6 Source file: src/gromacs/gmxana/gmx_rotacf.cpp (line 140) Fatal error: number of index elements not multiple of 2, these can not be atom doublets For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. -- 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
