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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>You don’t have writing permissions for the directory in which
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<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
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Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
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When the only tool you own is a hammer, every problem begins to resemble a
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
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gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Peter Nash<br>
<b>Sent:</b> Friday, 1 October 2010 5:36 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] grompp Input/Output Error<o:p></o:p></span></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'>Hey, <br>
<br>
I'm a new GROMACS user using 4.5.1... I'm working through whatever tutorials I
can find to learn the program. I'm having major problems using grompp...
No matter which tutorial I'm working through, when I run the program to create
a .trp file, I get an input/out error message. <br>
<br>
I'm going to use the offical Water demo as an example. I have the
conf.gro , spc216.pdb, topol.top, and grompp.mdp files in the default
directory. I run grompp using the following command line from within the
directory with the necessary input files:<br>
<br>
/home/[usr]/bin/gromacs/bin/grompp -v -f grompp.mdp -c conf.gro -p topol.top -o
topol_full.tpr <br>
<br>
I've also tried running it without the -v tag... Just to experiment. When
I enter the above command, I get the following output in the terminal: <br>
<br>
<br>
<br>
<br>
Ignoring obsolete mdp entry ‘title’<br>
Ignoring obsolete mdp entry ‘cpp’<br>
Ignoring obsolete mdp entry ‘domain-decomposition’<br>
Replacing old mdp entry ‘unconstrained-start’ by ‘continuation’<br>
Ignoring obsolete mdp entry ‘dihre-tau’<br>
Ignoring obsolete mdp entry ‘nstdihreout’<br>
Ignoring obsolete mdp entry ‘nstcheckpoint’<br>
Sorry couldn’t backup mdpout.mdp to ./#mdout.mdp.1#<br>
<br>
<br>
Program grompp, VERSION 4.5.1<br>
Source code file: futil.c, line: 459<br>
<br>
File input/output error:<br>
mdout.mdp<br>
<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
<br>
<br>
I'm not sure why the program is having an issue here since I'm following the
manual exactly. I also get a similar error whenever I try to run grompp using
any other .mdp file as well... No idea what the program is telling me, either. <br>
<br>
If anyone could give me input on this error, I'd greatly appreciate it.
Thank you! <br>
<br>
<o:p></o:p></p>
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