[gmx-users] need suggestion for building TMA

Mikko Hellgren Mikko.Hellgren at mbb.ki.se
Thu Mar 16 10:19:20 CET 2006


Hi, I would consider to try to use the program genconf in Gromacs. 
With this program you can stack and multiply a given coordinate 
file "like a small child playing with wooden blocks" - Gromacs manual.

Mikko Hellgren
PhD student at Karolinska Institutet
mikko.hellgren at ki.se 


Message: 3
Date: Wed, 15 Mar 2006 16:07:53 -0800
From: "David Mobley" <dmobley at gmail.com>
Subject: Re: [gmx-users] need suggestion for building TMA
(tetramethylammonium) topology and using as a general ion
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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<bc2c99750603151607y4709be4ela791e44fad1575b3 at mail.gmail.com>
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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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____________________________________________________
One cannot avoid making mistakes if one tries to produce a set of 
words, or of mathematical formulae, to describe nature. Nature is more 
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