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
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