[gmx-users] Odd error
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 18 20:27:43 CEST 2007
Christopher Stiles wrote:
> 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.
You're right. I don't understand. Anything changed in your environment?
Or could there be hidden characters in place of which a space is
printed? May be you can try to replace the space by another space.
Did you move the files between dos and unix machines?
The arguments are gobbled together into one, also in the editconf 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
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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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
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-request at gromacs.org.
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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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