[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion
dmobley at gmail.com
Thu Mar 16 01:07:53 CET 2006
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.
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 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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