[gmx-users] make_ndx error

[Albert]

On 01/26/2013 07:51 PM, Justin Lemkul wrote:
>
> Can you please post the following:
>
> 1. The groups printed in the make_ndx prompt
> 2. The output of gmxcheck on an index file created from your 
> coordinate file (created simply by typing 'q' at the prompt, i.e. not 
> creating any special groups)
>
> -Justin


make_ndx -f sys.pdb

  0 System              : 59870 atoms
   1 Protein             :  4746 atoms
   2 Protein-H           :  2329 atoms
   3 C-alpha             :   292 atoms
   4 Backbone            :   877 atoms
   5 MainChain           :  1170 atoms
   6 MainChain+Cb        :  1453 atoms
   7 MainChain+H         :  1455 atoms
   8 SideChain           :  3291 atoms
   9 SideChain-H         :  1159 atoms
  10 Prot-Masses         :  4746 atoms
  11 non-Protein         : 55124 atoms
  12 Other               : 18766 atoms
  13 NMA                 :     6 atoms
  14 POPC                : 18760 atoms
  15 CL                  :    39 atoms
  16 NA                  :    34 atoms
  17 Ion                 :    73 atoms
  18 NMA                 :     6 atoms
  19 POPC                : 18760 atoms
  20 CL                  :    39 atoms
  21 NA                  :    34 atoms
  22 Water               : 36285 atoms
  23 SOL                 : 36285 atoms
  24 non-Water           : 23585 atoms
  25 Water_and_ions      : 36358 atoms



gmxcheck_mpi -f md.xtc -n index.ndx

Item        #frames Timestep (ps)
Step           126    0.1
Time           126    0.1
Lambda           0
Coords         126    0.1
Velocities       0
Forces           0
Box            126    0.1
Contents of index file index.ndx
--------------------------------------------------
Nr.   Group               #Entries   First    Last
    0  System                 59870       1   59870
    1  Protein                 4746       1    4752
    2  Protein-H               2329       1    2332
    3  C-alpha                  292       8    2323
    4  Backbone                 877       2    2324
    5  MainChain               1170       2    2325
    6  MainChain+Cb            1453       2    2326
    7  MainChain+H             1455       2    4751
    8  SideChain               3291       1    4752
    9  SideChain-H             1159       1    2332
   10  Prot-Masses             4746       1    4752
   11  non-Protein            55124    4745   59870
   12  Other                  18766    4745   23512
   13  NMA                        6    4745    4750
   14  POPC                   18760    4753   23512
   15  CL                        39   23513   23585
   16  NA                        34   23518   23551
   17  Ion                       73   23513   23585
   18  NMA                        6    4745    4750
   19  POPC                   18760    4753   23512
   20  CL                        39   23513   23585
   21  NA                        34   23518   23551
   22  Water                  36285   23586   59870
   23  SOL                    36285   23586   59870
   24  non-Water              23585       1   23585
   25  Water_and_ions         36358   23586   23585