[gmx-users] grompp error with cpp
toma0052 at umn.edu
Sat Mar 24 18:27:26 CET 2007
Thanks for the reply,
I have tried changing the mdp file so it looks for the cpp in /lib/cpp,
/lib/cpp.exe, /bin/cpp, and /bin/cpp.exe and all of these produce the same
message as below, that the cpp file does not exist. It had worked when I ran
a simulation before with the mdp file as /lib/cpp, but I am not sure why it
is not working now. Should I just try to reinstall Gromacs?
On 24 Mar 2007, David van der Spoel wrote:
> toma0052 wrote:
> > Hello,
> > I just installed Gromacs on my windows machine under cygwin, and
> > everything seemed to go fine with the installation and whatnot.
> > when I tried to run a simulation, I obtained the error that Gromacs found
> > number of coordinates in my .top file to be 0, because it could not find
> > cpp. From the mailing list archives, I gathered that Gromacs was
> > for cpp in /lib/cpp whereas in cygwin the cpp is in /bin/cpp. So, as in
> > post, I created a link in /lib pointing to /bin/cpp. I ran a simulation,
> > everything went fine. Now, I am trying to run another simulation, and I
> > running into the same problem as before. When I execute grompp, I get
> > error:
> > Back Off! I just backed up md_shear_run.mdp to ./#md_shear_run.mdp.2#
> > checking input for internal consistency...
> > ...ling /lib/cpp
> > : No such file or directory
> > cpp exit code: 32512
> replace /lib/cpp with /bin/cpp (with or without .exe) in the mdp file
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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