type "which cpp" to know the location of cpp.
Another source of error could be your mdp file which is now in Windows'
format, using /r/n for a new line while Unix uses only /n.
Please use tools like dos2unix (a package shall be also available from
cygwin) to convert your mdp file.
Regards,
Yang Ye
toma0052 wrote:
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?
Thanks,
Mike
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.
Initially,
when I tried to run a simulation, I obtained the error that Gromacs found
the
number of coordinates in my .top file to be 0, because it could not find
the
cpp. From the mailing list archives, I gathered that Gromacs was
checking
for cpp in /lib/cpp whereas in cygwin the cpp is in /bin/cpp. So, as in
the
post, I created a link in /lib pointing to /bin/cpp. I ran a simulation,
and
everything went fine. Now, I am trying to run another simulation, and I
am
running into the same problem as before. When I execute grompp, I get
this
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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