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

[Simple]

Thanks for the kindly replies.

I write a python script to remove the water and then substitute the ion with 
TMA, Then add water again.
If I only add several TMA, It work well. Otherwise, the box have to enlarged, 
since the atoms went out of the box.

Then I find -ci option of the genbox may be work for me. 
It seem work. When I run an em on this system, no strange problem rise. 
although The density was a little large when more TMA were added in. It's not 
a big problem, which can solve with pressure coupled equilibrium.

It seem the problem is not difficult as I mentioned before. 
Is the method with genbox good enough? 

simple

> 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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