[gmx-users] Defining LA atoms in .gro file

[bharat gupta]

Dear GMX Users,

I am trying to perform QM/MM simulation for my system and I need to define
LA for the boundary between QM and MM region. I have the boundary regions
but I don't know how to add them in the gro file. Do I have to manually
modify the .gro file, if that's the case, adding, them manually how do I
renumber the rest of the atoms and residues? Here's what I have done:

 3715YWR   H21 3562   4.283   4.647   4.755 -1.1354  1.0843 -0.8713
  372XXX     LA 3563   2.475   3.856   2.040 -0.0020 -0.1066  0.1995
  373XXX     LA 3564   0.475   3.856   2.040 -0.0020 -0.1066  0.1995
  374XXX     LA 3565   1.475   3.856   2.040 -0.0020 -0.1066  0.1995
  375XXX     LA 3566   3.475   3.856   2.040 -0.0020 -0.1066  0.1995
  376XXX     LA 3567   0.875   3.856   2.040 -0.0020 -0.1066  0.1995
  377XXX     LA 3568   1.575   3.856   2.040 -0.0020 -0.1066  0.1995
  372SOL     OW 3563   3.414   3.445   2.243 -0.1786 -0.5561  0.4692
  372SOL    HW1 3564   3.479   3.440   2.167  0.5613 -1.1084  1.1215
  372SOL    HW2 3565   3.329   3.488   2.212  0.4389  0.0440 -0.4374
  373SOL     OW 3566   1.589   3.334   2.348  0.6300  0.1793 -0.1279
  373SOL    HW1 3567   1.639   3.413   2.384  1.2205  0.0166 -0.5746
  373SOL    HW2 3568   1.588   3.337   2.248 -1.5585  0.9770 -0.1508
  374SOL     OW 3569   5.280   6.227   4.070  0.5862 -0.1571 -0.6930

So, I added the LA atoms between atom no H21/3562 and OW/3563 manually.
Please let me whether this is the correct way of adding the LA atoms ?

Also, I need to modify the bond_types as well in the topology file to 5. Is
this the correct way:

1851  1853     2    gb_10
 1853  1854     5    gb_2
 1853  1855     5    gb_21
 1855  1856     5    gb_27
 1855  1862     5    gb_27
 1856  1857     5    gb_27
 1857  1858     5    gb_27
 1858  1859     5    gb_5
 1858  1860     5    gb_13
 1860  1861     5    gb_1
 1862  1863     5    gb_5
 1862  1864     2    gb_10
 1864  1865     2    gb_2

I haven't changed the values for C0 for the QM atoms but I have changed
their type to 5.

-- 
*Best Regards*
BM