[gmx-users] grompp Input/Output Error

[Justin A. Lemkul]

Peter Nash wrote:
> Hey,
> 
> 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.
> 
> 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:
> 
> /home/[usr]/bin/gromacs/bin/grompp -v -f grompp.mdp -c conf.gro -p 
> topol.top -o topol_full.tpr
> 
> 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:
> 
> 
> 
> 
> Ignoring obsolete mdp entry ‘title’
> Ignoring obsolete mdp entry ‘cpp’
> Ignoring obsolete mdp entry ‘domain-decomposition’
> Replacing old mdp entry ‘unconstrained-start’ by ‘continuation’
> Ignoring obsolete mdp entry ‘dihre-tau’
> Ignoring obsolete mdp entry ‘nstdihreout’
> Ignoring obsolete mdp entry ‘nstcheckpoint’
> Sorry couldn’t backup mdpout.mdp to ./#mdout.mdp.1#
> 
> 
> Program grompp, VERSION 4.5.1
> Source code file: futil.c, line: 459
> 
> File input/output error:
> mdout.mdp
> 
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> 
> 
> 
> 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.
> 
> If anyone could give me input on this error, I'd greatly appreciate it.  
> Thank you!
> 
> 

Looks like you don't have write permissions in the directory where you're 
running grompp.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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