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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
>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
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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
>
>
>--
>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
>_______________________________________________
>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
_______________________________________________
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