[gmx-users] Ice box

[Fernando Mattio]

 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:
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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