[gmx-users] need suggestion for building TMA (tetramethylammonium) topology and using as a general ion
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 15 08:58:29 CET 2006
> 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
> 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.
> 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
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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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