[gmx-users] Odd error
Christopher Stiles
CS145331 at albany.edu
Tue Sep 18 20:33:47 CEST 2007
Very good yes something was odd with the spaces, I had been making a walk
through on how to exactly perform my simulation and I was testing the
commands that I had put onto a web site and apparently there must be some
sort of funny spaces in there, but when I removed the spaces and replaced
them the commands worked properly again.
Thank you again,
~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 2:28 PM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] Odd error
>
>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
>>>>
>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------------
>-
>>>>
>>>> _______________________________________________
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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
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>>
>>
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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!
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