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

[Lucio Montero]

If you are using the GROMOS96, the forcefield files are ffG????.*. ffgmx are 
for the GROMACS forcefield (that is deprecated). The forcefield file titles 
are listed in the file FF.dat in the gromacs topology directory. Here are 
the contents of my FF.dat file:
11
ffG43a1  GROMOS96 43a1 force field
ffG43b1  GROMOS96 43b1 vacuum force field
ffG43a2  GROMOS96 43a2 force field (improved alkane dihedrals)
ffG45a3  GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
ffG53a5  GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
ffG53a6  GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
ffoplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
ffgmx    [DEPRECATED] Gromacs force field (see manual)
ffgmx2   [DEPRECATED] Gromacs force field with hydrogens for NMR
ffencadv Encad all-atom force field, using scaled-down vacuum charges
ffencads Encad all-atom force field, using full solvent charges
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Hope this helps.

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From: "Fabian Homberg" <homberg.fabian at googlemail.com>
Sent: Saturday, September 27, 2008 7:09 AM
To: <gmx-users at gromacs.org>
Subject: [gmx-users] Integration of a carbonate ion to GROMACS V3.3

> 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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