[gmx-users] define a new residue

[Shima Arasteh]

Hi dear gmx friends,

I got the parameters of formyl-valine through the CHARMM website. Now I need to define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file. To set the correct charges for atoms, I used the CHARMM output. In order to define FVAL to rtp file, I added these lines as below:

CN    C    0.349    0
    ON    O    -0.494    1
    H1    HC    0.100    2
    N    NH1    -0.423    3
    HN    H    0.09    4
    CA    CT1    0.144    5
    HA    HB    0.09    6
    CB    CT1    -0.097    7
    HB    HA    0.09    8
    CG1    CT3    -0.268    9
    HG11    HA    0.09    10
    HG12    HA    0.09    11
    HG13    HA    0.09    12
    CG2    CT3    -0.268    13
    HG21    HA    0.09    14
    HG22    HA    0.09    15
    HG23    HA    0.09    16
    C    C    0.209    17
    O    O    -0.395    18

As you see I omitted the H connected to Carboxyl. Now the total charge of the new-defined residue is not zero (-0.333) . How can I correct it? 


I would appreciate you for your suggestions.
Thanks in advance.

Sincerely,
Shima