[gmx-users] on the itp file

[Brett]

Dear All,

In the on-line protein-ligand md tutorial, related to the drg.itp file, there is





"Let's take a look at the [ atoms ] section of our JZ4 topology:

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  JZ4      C4     1    0.000  15.0350
     2       CH2     1  JZ4     C14     2    0.059  14.0270
     3       CH2     1  JZ4     C13     2    0.060  14.0270
     4         C     1  JZ4     C12     2   -0.041  12.0110
     5       CR1     1  JZ4     C11     2   -0.026  12.0110
     6        HC     1  JZ4     H11     2    0.006   1.0080
     7       CR1     1  JZ4      C7     2   -0.026  12.0110
     8        HC     1  JZ4      H7     2    0.006   1.0080
     9       CR1     1  JZ4      C8     2   -0.026  12.0110
    10        HC     1  JZ4      H8     2    0.007   1.0080
    11       CR1     1  JZ4      C9     2   -0.026  12.0110
    12        HC     1  JZ4      H9     2    0.007   1.0080
    13         C     1  JZ4     C10     3    0.137  12.0110
    14        OA     1  JZ4     OAB     3   -0.172  15.9994
    15         H     1  JZ4     HAB     3    0.035   1.0080".

May I ask, for the drg.itp file, we only need contain the  [ atoms ] section, all we should contain every sections of the original drg.itp file?

Secondly, suppose my ligand itp was not got by the traditional gromacs forcefiled, in this situation should we modify the atom types database we got when we originally installed the gromacs to include the atom types specified for the ligand, or we can have the ligand.itp contains a section with the specific ligand atom types information supplied?

Brett