[gmx-users] Odd error

[Christopher Stiles]

If you look at the error it is including the next part of the command with
the previous. If you look the error is the following: 

###########################
File input/output error:

SWNT_6_6_144.gro -cs.gro
###########################

It should evaluate one at a time "-cs" should not have ".gro" affixed to it
when the command is evaluated. Also I looked it over a few times there is no
typos and all the files are in the directory in which I am running the
command.

To give another example it happened when I ran the editconf as well:

##################
-bash-3.00$ editconf -f SWNT_6_6_144.pdb -o SWNT_6_6_144.gro -d 1.0
                         :-)  G  R  O  M  A  C  S  (-:
.
.
.
-------------------------------------------------------
Program editconf, VERSION 3.3.1
Source code file: statutil.c, line: 799

Invalid command line argument:
1.0
-------------------------------------------------------
##################

Mind you earlier today I ran these exact same commands with the same files
and it worked fine.

Thank you,
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE) 
State University of New York, Albany, New York 12203, USA

>-----Original Message-----
>From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>On Behalf Of David van der Spoel
>Sent: Tuesday, September 18, 2007 2:05 PM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] Odd error
>
>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.
>spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
>_______________________________________________
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