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

[David]

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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