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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] >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: [EMAIL PROTECTED] [mailto:gmx-users- >[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 [email protected] >>>> 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 [email protected] >>> 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 >> >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected] >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 _______________________________________________ gmx-users mailing list [email protected] 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
