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.
Thank you,
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
