[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion

[David Mobley]

Another approach to adding it might be to take your protein, before
solvating it, and write a script to add some number of TMA molecules
randomly distributed throughout the box. Then solvate in the usual
way. This obviously would take some work, though.

David


On 3/14/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Simple wrote:
> >    In chemical experiments that ion effect is important,tetramethylammonium
> > (TMA) is usually added to compensate the ion strength.I would like to test it
> > in simulation. There were experiments showed that the ion contributed a lot
> > to the distinct results.
> >    I looked around but not found a topology  of TMA is ready-to-use. So I
> > decided to create one. Thanks for  Schuettelkopf and  van Aalten, The PRODRG
> > server do all the things. Since I am still a newbie for Gromacs and not very
> > confident with my chemistry knowledge,I wonder if the parameters in the
> > topology is rational? (The topology is present at the last.)
> compare it to topologies for lipid headgroups available from the
> Tieleman website
>
> >
> >    The second problem is how can I use this topology as a general ion.
> >    It is difficult to add them into gro file by hand because I should put a
> > lot of TMA into the solutions.
> genion will not be able to handle this because it is too big (genion
> replaces water molecules by ions). You will need to use e.g. genconf
> and/or genbox, but there is no ready solution. Maybe you can do a simple
> simulation of a TMA solution and then dissolve the protein in that.
>
> >    If I can treat it as a general ion, such as Na or Mg,etc, which will save
> > me a lot. My straight forward thought is to add the information into the
> > ion.itp, so genion can find and use it. If this work, I believe others would
> > also benefit from it, since TMA is so widely used. Does it work well?
> >    If this method is not so good,I think I can write a simple program to
> > substitute the ion in the gro with TMA. Of course, I would rewrite the
> > position of all the TMA atom and renumber the atom. For the top file, I need
> > only replace the ion name with TMA.
> >    What should I pay a lot of attention to for these method?
> >
> >    If something I wrote are totally wrong, please not hesitate to let me know.
> > Thanks.
> >
> > topology created by PRODRG
> > ;
> > ;       This file was generated by PRODRG version 051202.0518
> > ;       PRODRG written/copyrighted by Daan van Aalten
> > ;
> > ;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> > ;
> > ;       When using this software in a publication, cite:
> > ;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> > ;       PRODRG - a tool for high-throughput crystallography
> > ;       of protein-ligand complexes.
> > ;       Acta Crystallogr. D60, 1355--1363.
> > ;
> > ;
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > TMA      3
> >
> > [ atoms ]
> > ;   nr      type  resnr resid  atom  cgnr   charge     mass
> >      1       CH3     1  TMA      C1     1    0.076  15.0350
> >      2        NL     1  TMA      N1     1    0.696  14.0067
> >      3       CH3     1  TMA      C3     1    0.076  15.0350
> >      4       CH3     1  TMA      C4     1    0.076  15.0350
> >      5       CH3     1  TMA      C2     1    0.076  15.0350
> >
> > [ bonds ]
> > ; ai  aj  fu    c0, c1, ...
> >    1   2   1    0.147    376560.0    0.147    376560.0 ;    C1   N1
> >    2   3   1    0.147    376560.0    0.147    376560.0 ;    N1   C3
> >    2   4   1    0.147    376560.0    0.147    376560.0 ;    N1   C4
> >    2   5   1    0.147    376560.0    0.147    376560.0 ;    N1   C2
> >
> > [ pairs ]
> > ; ai  aj  fu    c0, c1, ...
> >
> > [ angles ]
> > ; ai  aj  ak  fu    c0, c1, ...
> >    1   2   3   1    109.5       376.6    109.5       376.6 ;    C1   N1   C3
> >    1   2   4   1    109.5       376.6    109.5       376.6 ;    C1   N1   C4
> >    1   2   5   1    109.5       376.6    109.5       376.6 ;    C1   N1   C2
> >    3   2   4   1    109.5       376.6    109.5       376.6 ;    C3   N1   C4
> >    3   2   5   1    109.5       376.6    109.5       376.6 ;    C3   N1   C2
> >    4   2   5   1    109.5       376.6    109.5       376.6 ;    C4   N1   C2
> >
> > [ dihedrals ]
> > ; ai  aj  ak  al  fu    c0, c1, m, ...
> >    2   1   3   4   2     35.3  836.8       35.3  836.8   ; imp    N1   C1   C3
> > C4
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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