[gmx-users] Using a rtp file for sugar

[David]

On Wed, 2005-10-05 at 16:48 +0200, Fernando Mattio wrote:
>        Hi again,
>        I just found pdb files of sugars in
> http://www.nyu.edu/pages/mathmol/library/sugars/
>        So I think the next step is to use the genbox, right? With this
> should be possible to multiply my sugar molecules and to put them in
> random positions. Well I am not sure about this because I am new as
> Gromac user, so any consideration about would be helpful for me.
You can use genconf for the sugars and then genbox for solvating them.
You can generate a topology using prodrg.


>        Thanks again,
>        Fernando Mattio
> 
> 2005/10/5, Fernando Mattio <mattiofer at gmail.com>:
>             Hi Tsjerk and Gromacs users,
>            Thank you for your answer Tsjerk, but I am still a little
>         bit confused. What I would like to have is a protein in a box
>         of water, with molecules of sugar present in the system, I
>         mean in random positions. So I think I don´t need sugar
>         chains...  
>            What I understood from your answer is that I need an .itp
>         file of sugar to be added in the topology file, is it right?
>         The problem is that I could not find in the Gromacs files an
>         itp file for sugar, only .rtp, so do I have to create it or is
>         it already done somewhere that I could not find? 
>         
>           Sugars
>         
>         
>         GALB 
>         ffgmx.rtp
>         - 
>         galactose-
>         B
>         C6H10O5
>         -
>         GLCA 
>         ffgmx.rtp
>         - 
>         glucose-A
>         C6H10O5
>         -
>         GLCB 
>         ffgmx.rtp
>         - 
>         glucose-B
>         C6H10O5
>         -
>         
>         
>            And then to "multiply" my molecules of sugar and to add
>         them to my system in random positions, what programs should I
>         use?
>           
>            Thank you very much in advance,
>            Fernando Mattio
>         
>         
>         
>         2005/10/5, Tsjerk Wassenaar <tsjerkw at gmail.com>:
>                 Hi Fernando,
>                 
>                 Unless you're trying to build sugar chains, you don't
>                 need to make building blocks in the .rtp file. It is
>                 better to use .itp files for them. Also, it's better
>                 not to use the gmx force field, but rather the GROMOS
>                 one, for which there should be good sugar parameters
>                 available (by Roberto Lins).
>                 And genbox doesn't use the .rtp file, it's only used
>                 by pdb2gmx. Genbox will insert molecules from a
>                 structure file (gro, pdb).
>                 
>                 Cheers,
>                 
>                 Tsjerk
>                 
>                 
>                 
>                 On 10/5/05, Fernando Mattio <mattiofer at gmail.com>
>                 wrote:
>                         Dear Gromacs users,
>                         
>                         I would like to insert some molecules of sugar
>                         in a box with protein and water .  So my idea
>                         was to use the ffgmx.rtp file, but copying
>                         only  the information of for example GALB and
>                         saving it as other .rtp file. It is the first
>                         time that I am dealing with this kind of
>                         topology file, and I would like to know if it
>                         is the right way of using the Gromacs Building
>                         Blocks.
>                         Then with genbox I think it is possible to
>                         create other sugar molecules from the .rtp
>                         file and to add them to my system, is it
>                         right?
>                         
>                         Thank you very much in advance!
>                         Fernando Mattio
>                         
>                         
>                         
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>                 
>                 
>                 
>                 -- 
>                 
>                 Tsjerk A. Wassenaar, M.Sc.
>                 Groningen Biomolecular Sciences and Biotechnology
>                 Institute (GBB)
>                 Dept. of Biophysical Chemistry 
>                 University of Groningen
>                 Nijenborgh 4
>                 9747AG Groningen, The Netherlands
>                 +31 50 363 4336
>         
> 
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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://xray.bmc.uu.se/~spoel
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