[gmx-users] grompp error with cpp

[Yang Ye]

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
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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>
>
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