[gmx-users] Chage modifications with pdb2gmx

[Krzeminski]

Hi Gromacs users,

I tried to find the solution of this problem in the forum, but I did not 
manage...

Actually, I created a new building block for a residue in the rtp file. This 
following is an extract of this residue:

   N1	    NR    -0.28000     8
   H1     H       0.28000     8     --> HERE
   C6     C        0.38000     9
   O6	    O       -0.38000     9
   C5     C        0.00000    10
   N7	    NR     -0.36000    10
   C8     CR1    0.36000    10
  C2*    CH1    0.15000    11
  O2*    OA    -0.54800    11

When I launch pdb2gmx, I have got a number of charges that is a float instead 
of an integer (as expected). I found the origin of this error looking at the 
generated itp file:

27    NR    1    GNP     N1      9      -0.28    14.0067   ; qtot -3.28
28    H      1    GNP     H1     10   -0.15    1.008   ; qtot -3.43  --> HERE
29    C      1    GNP     C6     11       0.38     12.011   ; qtot -3.05
30    O      1    GNP     O6     11      -0.38    15.9994   ; qtot -3.43
31    C      1    GNP     C5     12          0     12.011   ; qtot -3.43
32    NR    1    GNP     N7     12      -0.36    14.0067   ; qtot -3.79
33    CR1  1    GNP     C8     12       0.36     13.019   ; qtot -3.43
34    CH1  1    GNP    C2*     13       0.15     13.019   ; qtot -3.28
35    OA    1    GNP    O2*     13     -0.548    15.9994   ; qtot -3.828

First of all, the charge beared by the hydrogen H1 has been modified (from 
0.28000 to -15.0). Moreover, the group this atom belonged to has been 
modified too (from 8 to 9)!

Does anybody one have an idea ?

Thanks in advance,
Mickael