Christopher Stiles wrote:
I have been using Gromacs for some time now and actually today I have
been using it without a problem but then all a sudden commands that I
had been using stopped functioning properly. The following is an example
of this:
############################################
-bash-3.00$ genbox -cp SWNT_6_6_144.gro -cs -o SWNT_6_6_144_b4em.gro -p
SWNT_6_6
_144.top -maxsol 804
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen , The Netherlands .
Copyright (c) 2001-2006, 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 SWNT_6_6_144.gro -cs.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 SWNT_6_6_144_b4em.gro Output Generic structure: gro g96 pdb xml
-p SWNT_6_6_144.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 804 maximum number of solvent molecules to add if
they fit in the box. If zero (default) this is
ignored
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
-------------------------------------------------------
Program genbox, VERSION 3.3.1
Source code file: futil.c, line: 340
File input/output error:
SWNT_6_6_144.gro -cs.gro
-------------------------------------------------------
"I Live the Life They Wish They Did" (Tricky)
##############################################
Has any one else experience such a problem? This is not limited to just
this one command, it seams that it is now not reading the commands
properly. I have restarted the server in an vain hopes it would fix its
self but this has had no effect.
it can't find the file. you may have mistyped its name are added a space
in the middle.
Thank you,
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York , Albany , New York 12203 , USA
------------------------------------------------------------------------
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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