[gmx-users] Ice box

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 25 12:23:17 CEST 2005


On Tue, 2005-10-25 at 11:36 +0200, Fernando Mattio wrote:
>       Dear Gromacs users,
>        First thank you Erik and David, now the mkice is running. But
> unfortunately I couldn´t solve my problem yet. With this mkice option
> I could again generate ice crystals (.gro file), but as I wrote
> before, I already have pdb files with the ice crystals. And using
> editconf I can also create from  my pdb files the .gro files .
>      My problem is really the topology file, because when I tried to
> use the pdb2gmx I had the following fatal error:

don't use pdb2gmx, it's only for proteins. do it manually. ch. 5.
> FATAL ERROR: Residue "OHH" not found in residue topology database
>      I tried then the prodrg server, but it doesn´t work with only H
> anf O atoms...
>      And I also tried to use x2top from my .gro file but I got again a
> fatal error:
> FATAL ERROR: Library file ffG43a1 not found in current dir nor in
> default directories. (You can set the directories to search with
> GMXLIB path variable).
>      I read the Chapter 5, and I got the general idea of how create an
> itp file... But I don´t know where to find informations about
> dihedrals, bonds, angles and pairs from my pdb files. And I really don
> ´t know if it´s the easiest way to solve my problem, because I am such
> a new user. Maybe to try to add water as a residue should be a
> reasonable way, but I still have to learn how to do that. And I am not
> sure if the pdb2gmx would work. So please any advice would be very
> helpful for me.
>      Thank you very much in advance,
>      Fernando Mattio
> 
> 2005/10/24, David van der Spoel <spoel at xray.bmc.uu.se>:
>         On Mon, 2005-10-24 at 10:14 +0200, Fernando Mattio wrote:
>         >    Hi Erick,
>         >    I searched in my src directory on my computer and there
>         is no mkice
>         > file, I also searched it in contributions folders but I
>         couldn´t 
>         > find... So is there any other way to download this make
>         mkice file? Is
>         > it avaiable somewhere?
>         cd src/contrib
>         make mkice
>         
>         >
>         >    Thank you very much in advance.
>         >    Fernando Mattio 
>         >
>         > 2005/10/11, Erik Lindahl <lindahl at sbc.su.se>:
>         >         Hi,
>         >
>         >         I fixed the mkice program so it compiles, just
>         before
>         >         releasing 
>         >         version 3.3.
>         >
>         >         Go to src/contrib, and issue "make mkice". Then run
>         "mkice -h"
>         >         to get
>         >         help on creating ice crystals.
>         >
>         >         Cheers, 
>         >
>         >         Erik
>         >
>         >         On Oct 10, 2005, at 3:59 PM, Fernando Mattio wrote:
>         >
>         >         > Dear gromacs users,
>         >         > I would like to know if it is possible with
>         gromacs to 
>         >         create a box
>         >         > not with water and protein, but only with ice. I
>         couldn´t
>         >         generate
>         >         > a topology of the ice in the prodrg sever, and the
>         command
>         >         pdb2gmx 
>         >         > didn´t work... So I am wondering if it is
>         possible...
>         >         > Many thanks in advance,
>         >         > Fernando Mattio
>         >         > _______________________________________________ 
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>         >
>         -----------------------------------------------------------
>         >         Erik Lindahl  <lindahl at sbc.su.se>
>         >         Assistant Professor, Stockholm Bioinformatics
>         Center 
>         >         Stockholm University, SE 106 91 Stockholm
>         >         Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>         >
>         >
>         >
>         >
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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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>         
>         
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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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