[gmx-users] Using make_ndx

[Lili Peng]

Hi everyone,

I'm trying to figure out the right commands for make_ndx so to generate the
correct index.ndx file for g_bond analysis.  From my PDB file:

ATOM      1  BN0 GGA X   1     107.255  17.133  66.368  1.00  0.00      P1
C
ATOM      2  SC1 GGA X   1     110.304  14.942  66.116  1.00  0.00      P1
C
ATOM      3  SC2 GGA X   1     113.632  15.318  65.904  1.00  0.00      P1
C
ATOM      4  SC3 GGA X   1     114.063  12.624  65.310  1.00  0.00      P1
C
ATOM      5  BN0 GGA X   2     108.171  20.156  68.028  1.00  0.00      P1
C
ATOM      6  SC1 GGA X   2     109.535  18.753  71.242  1.00  0.00      P1
C
ATOM      7  SC2 GGA X   2     112.445  17.547  72.396  1.00  0.00      P1
C
ATOM      8  SC3 GGA X   2     111.301  16.592  74.758  1.00  0.00      P1
C
ATOM      9  BN0 GGA X   3     110.843  21.726  66.258  1.00  0.00      P1
C
ATOM     10  SC1 GGA X   3     111.984  24.201  68.852  1.00  0.00      P1
C
ATOM     11  SC2 GGA X   3     114.049  24.264  71.496  1.00  0.00      P1
C
ATOM     12  SC3 GGA X   3     113.142  26.763  72.351  1.00  0.00      P1
C
..<rest of PDB file not included>...

Say I want to group together atoms SC1, SC2, and SC3 from all GGA residues
in make_ndx:

  0 System              : 19699 atoms
  1 GGA                 :   472 atoms
  2 DRG                 :   324 atoms
  3 W                   : 18669 atoms
  4 ION                 :   234 atoms

I typed in:

> r GGA & t SC1 | r GGA & t SC2 | r GGA & t SC3

Found 472 atoms with residue name GGA
Found 36 atoms with type SC1
Merged two groups with AND: 472 36 -> 0
Found 472 atoms with residue name GGA
Merged two groups with OR: 0 472 -> 472
Found 24 atoms with type SC2
Merged two groups with AND: 472 24 -> 0
Found 472 atoms with residue name GGA
Merged two groups with OR: 0 472 -> 472
Found 0 atoms with type SC3

  5 GGA_&_SC1_GGA_&_SC2_GGA:   472 atoms

However,  make_ndx "found 0 atoms with type SC3".  I'm not sure if I'm doing
this correctly.

If anyone has any insight, I would be most appreciative.

Thanks,
L
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