[gmx-users] grompp problem with cpp -- 'does not match topology'

[yli at hcg.bmb.uga.edu]

Yes, you are exactly right. I created the mdp file in windows and moved to
LINUX. That caused the problem.
Thank you.

> On Wed, 2004-06-30 at 18:40, yli at hcg.bmb.uga.edu wrote:
>> I encountered the problem when running grompp:
>>
>> -------------------------------------
>> checking input for internal consistency...
>> ...ling /usr/bin/cpp
>> : No such file or directory
>> cpp exit code: 32512
>>  recd271.top > gromppdkR4fG'/top -DFLEX_SPC
>> ' command is defined in the .mdp file
>
>
> the command looks weird. Start by removing the cpp line. It will be
> found anyway. Could this be a mdp file that is moved from a dos box to
> your linux box? (i.e. strange linefeeds etc.)
>
>
>> processing topology...
>> processing coordinates...
>> Fatal error: number of coordinates in coordinate file
>> (recd271_genbox.gro,
>> 27284)
>>              does not match topology (recd271.top, 0)
>> ---------------------------------------
>>
>> I'm sure the cpp is installed in my Redhat LINUX 9.0 /usr/bin
>> My top file also looks fine. It contains 1 protein molecules and 8214
>> solvent molecules.
>>
>> I have no idea how to fix this. I searched the mailing list but didn't
>> find a solution.
>>
>> The mdp file is as follows:
>> title       = EM_for_recd271
>> cpp         = /usr/bin/cpp
>> define      = -DFLEX_SPC
>> integrator  = cg
>> nsteps      = 10000
>> constraints  = none
>> nstlist     = 10
>> ns_type     = grid
>> rlist       = 1.0
>> rcoulomb    = 1.0
>> rvdw        = 1.0
>> emtol       = 100
>> emstep      = 0.01
>> nstcgsteep  = 1000
>>
>>
>> I will appreciate any help from you.
>>
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> --
> 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://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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