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

yli at hcg.bmb.uga.edu yli at hcg.bmb.uga.edu
Wed Jun 30 18:40:09 CEST 2004

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
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file (recd271_genbox.gro,
             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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