[gmx-users] Integration of a carbonate ion to GROMACS V3.3

[Fabian Homberg]

Dear GROMACS-team,

i have a problem with the integration of a carbonate ion (CO3 ^2-) to
GROMACS, because i want to simulate a mixture of tip4p-water with
solvated potassium carbonate and the carbonate ion is not integrated
in the standard version.
After having read  „balamurugan r biobee at rediffmail.com"'s problem,
which is almost the same i have, i tried to integrate:

 [CO3]
  [atoms]
 OAA OM  -0.221  0
 CAC  C  0.494  1
 OAB  OM  -0.221 0
 OAD  OM  -0.052 2

to the ffgmx.rtp-file (I am using the GROMOS-96 standard force field: ffgmx.*).
Then i went on with adding:

[ moleculetype ]
; molname       nrexcl
CO3-            1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge   mass
1       CO3-    1       CO3-            CO3-     1      -2       60.00800

to the ions.itp-file.
Finally i tried to get the system ready for an energy-minimization
with the command
"grompp -f em -p topol -o topol -c conf -n index",
but then a fatal error occurred:
"No such moleculetype CO3"

So i went on trying to integrate:

[ moleculetype ]
; Name nrexcl
CO3      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
    1        OM     1  CO3     OAA     1   -0.221  15.9994
    2         C     1  CO3     CAC     1    0.494  12.0110
    3        OM     1  CO3     OAB     1   -0.221  15.9994
    4        OM     1  CO3     OAD     1   -0.052  15.9994

[ bonds ]
; ai  aj  fu    c0, c1, ...
  1   2   1    0.125    418400.0    0.125    418400.0 ;   OAA  CAC
  2   3   1    0.125    418400.0    0.125    418400.0 ;   CAC  OAB
  2   4   1    0.125    418400.0    0.125    418400.0 ;   CAC  OAD

[ pairs ]
; ai  aj  fu    c0, c1, ...

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
  1   2   3   1    126.0       502.1    126.0       502.1 ;   OAA  CAC  OAB
  1   2   4   1    126.0       502.1    126.0       502.1 ;   OAA  CAC  OAD
  3   2   4   1    126.0       502.1    126.0       502.1 ;   OAB  CAC  OAD

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
  2   4   3   1   2      0.0 1673.6 0      0.0 1673.6 0 ; imp   CAC
OAD  OAB  OAA
to the .itp-file, but it still doesn't work.

Do you have advice to solve this problem?


Best regards

Fabian Homberg
Student assistant at
Lehrstuhl für Thermodynamik (LTD)
TU Kaiserslautern, Germany