[gmx-users] rotacf error

[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.

-- 
*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*
-------------- next part --------------
 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:   146    Protein residues
There are: 23993      Water residues
There are:   196        Ion 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' nr    Enter: 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) has    93 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) has    84 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.