Hello,
It turns out !genprism does work, it was just another input error on my
part. !genbox however doesn't, and !rgenbox too. The directory you posted
isn't on my computer. In fact I can't find any files called "readme" at all.
I get many many lines of this with rgenbox:
xform: (standard input): warning - empty file
xform: (!rgenbox red_tile tile_a 1 1 .1 -b .025 | xform -t 1 1
-.1): warning - empty file
sh: rgenbox: not found
xform: (standard input): warning - empty file
xform: (!rgenbox white_tile tile_a 1 1 .1 -b .025 | xform -t 0 1
-.1): warning - empty file
sh: rgenbox: not found
...or this with genbox:
G R O M A C S (-:
Green Red Orange Magenta Azure Cyan Skyblue
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) genbox (-:
Option Filename Type Description
···
------------------------------------------------------------
-cp protein.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-cs spc216.gro Input, Opt., Lib. Generic structure: gro g96 pdb tpr
tpb
tpa xml
-ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-o out.gro Output Generic structure: gro g96 pdb xml
-p topol.top In/Out, Opt. Topology file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-box vector 0 0 0 box size
-nmol int 0 no of extra molecules to insert
-try int 10 try inserting -nmol*-try times
-seed int 1997 random generator seed
-vdwd real 0.105 default vdwaals distance
-shell real 0 thickness of optional water layer around solute
-maxsol int 0 maximum number of solvent molecules to add if
they fit in the box. If zero (default) this is
ignored
-[no]vel bool no keep velocities from input solute and solvent
-------------------------------------------------------
Program genbox, VERSION 3.3.3
Source code file: ../../../../src/gmxlib/statutil.c, line: 797
Invalid command line argument:
red_tile
-------------------------------------------------------
"Take Dehydrated Water On Your Desert Trips" (Space Quest III)
xform: (standard input): warning - empty file
xform: (!genbox red_tile tile_a 1 1 .1 -b .025 | xform -t 0 0
-.1): warning - empty file
Could you walk me through what to do, in order to get Radiance's !genbox
working, instead of, what I'm assuming, is another program for
who-knows-what?
Thank you!
Nick
Lars O. Grobe wrote:
*
*>>* Has this command changed too? (such as rview to rvu)
*>*
*>* On Linux systems, there already exists a command genbox. So the package
*>* maintainers (I guess you use a debian or ubuntu setup?) have to rename
*>* these tools (I would guess to rgenbox, rgenprism) to avoid
*>* unpredicteable behaviour. The source tree at radsite/radiance-online
*>* doesn't reflect these changes, the documentation doesn't do it neither.
*
On Debian and Ubuntu these changes are documented in
/usr/share/doc/radiance/README.Debian
There's also described how to modify $PATH to get the old function back.
Cheers,
Bernd
--
Bernd Zeimetz Debian GNU/Linux Developer
GPG Fingerprint: 06C8 C9A2 EAAD E37E 5B2C BE93 067A AD04 C93B FF79