[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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--
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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