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

[David van der Spoel]

Fabian Homberg wrote:
> 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?
> 

yes. use a virtual site to make the C position instead of adding the 
improper.

> 
> Best regards
> 
> Fabian Homberg
> Student assistant at
> Lehrstuhl für Thermodynamik (LTD)
> TU Kaiserslautern, Germany
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se