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
--
========================================
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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