Dear Gromacs users,<br>
First thank you Erik and David, now the
mkice is running. But unfortunately I couldnīt 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 .<br>
My problem is really the topology file,
because when I tried to use the pdb2gmx I had the following fatal error:<br>
FATAL ERROR: Residue "OHH" not found in residue topology database<br>
I tried then the prodrg server, but it doesnīt work with only H anf O atoms...<br>
And I also tried to use x2top from my .gro file but I got again a fatal error:<br>
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).<br>
I read the Chapter 5, and I got the general
idea of how create an itp file... But I donīt know where to find
informations about dihedrals, bonds, angles and pairs from my pdb
files. And I really donīt know if itīs 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.<br>
Thank you very much in advance,<br>
Fernando Mattio<br><br><div><span class="gmail_quote">2005/10/24, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Mon, 2005-10-24 at 10:14 +0200, Fernando Mattio wrote:<br>> Hi Erick,<br>> I searched in my src directory on my computer and there is no mkice<br>> file, I also searched it in contributions folders but I couldnīt
<br>> find... So is there any other way to download this make mkice file? Is<br>> it avaiable somewhere?<br>cd src/contrib<br>make mkice<br><br>><br>> Thank you very much in advance.<br>> Fernando Mattio
<br>><br>> 2005/10/11, Erik Lindahl <<a href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</a>>:<br>> Hi,<br>><br>> I fixed the mkice program so it compiles, just before<br>> releasing
<br>> version 3.3.<br>><br>> Go to src/contrib, and issue "make mkice". Then run "mkice -h"<br>> to get<br>> help on creating ice crystals.<br>><br>> Cheers,
<br>><br>> Erik<br>><br>> On Oct 10, 2005, at 3:59 PM, Fernando Mattio wrote:<br>><br>> > Dear gromacs users,<br>> > I would like to know if it is possible with gromacs to
<br>> create a box<br>> > not with water and protein, but only with ice. I couldnīt<br>> generate<br>> > a topology of the ice in the prodrg sever, and the command<br>> pdb2gmx
<br>> > didnīt work... So I am wondering if it is possible...<br>> > Many thanks in advance,<br>> > Fernando Mattio<br>> > _______________________________________________
<br>> > gmx-users mailing list<br>> > <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
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</a>.<br>><br>> -----------------------------------------------------------<br>> Erik Lindahl <<a href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</a>><br>> Assistant Professor, Stockholm Bioinformatics Center
<br>> Stockholm University, SE 106 91 Stockholm<br>> Phone: +46 8 5537 8564 Fax: +46 8 5537 8214<br>><br>><br>><br>><br>> _______________________________________________<br>
> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>><br>> _______________________________________________
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<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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