[gmx-users] choosing appropriate force field

[elham tazikeh]

Dear Justin
thanks for your help

i used of *ATB server* for making *.itp* file for SAL (salicylic acid), as
below:

[ moleculetype ]
; Name   nrexcl
_N4Y     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OA    1    _N4Y    O10    1   -0.546  15.9994
    2     H    1    _N4Y    H16    1    0.469   1.0080
    3     C    1    _N4Y     C8    1    0.643  12.0110
    4     O    1    _N4Y     O9    1   -0.566  15.9994      ;  0.000
    5     C    1    _N4Y     C3    2   -0.221  12.0110
    6     C    1    _N4Y     C2    2    0.388  12.0110
    7    OA    1    _N4Y     O7    2   -0.604  15.9994
    8     H    1    _N4Y    H15    2    0.437   1.0080      ;  0.000
    9     C    1    _N4Y     C1    3   -0.266  12.0110
   10    HC    1    _N4Y    H11    3    0.175   1.0080
   11     C    1    _N4Y     C6    3   -0.049  12.0110
   12    HC    1    _N4Y    H14    3    0.140   1.0080      ;  0.000
   13     C    1    _N4Y     C5    4   -0.201  12.0110
   14    HC    1    _N4Y    H13    4    0.141   1.0080
   15     C    1    _N4Y     C4    4   -0.073  12.0110
   16    HC    1    _N4Y    H12    4    0.133   1.0080      ;  0.000
; total charge of the molecule:   0.000


here, i have a question:
in ATB server , there are 2 force field as default:* gromos 54A7 , gromos
53A6*
i did not see other force field,right?
for my simulation, can i choose *gromos43a1* or i have to choosing the same
force field (as ATB), i mean i must choose gromos 54A7?

on theother hand, Formats in ATB,were:
Gromacs
Gromos 11
Gromos 96

for my study, i choosed *Gromacs* as format in ATB , is it correct?

finally, for SAL molecule ; there is SAL in ATB as default, and i used of
it without loading of anywhere (same PRODRG)
is this correct?


at the end, shoul i  change *pdb* format (produced by ATB) to *gro* with
*editconf* tool in gromacs and then *copy* et the end of my  protein
coordinate file?
or
change my *complex.pdb* (get from RCSB) format to *coordinate.gro?*

i really appriciate for your advise

cheers