[gmx-users] Grompp error

"Cíntia C. Vequi-Suplicy" cintiadevequi at gmail.com
Tue Aug 25 18:29:02 CEST 2009


I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dppc128.top > gromppzJXISa'cpp
' command is defined in the .mdp file
* Important: if you do not have a c-preprocessor installed, *
* you MUST run grompp with the "-pp" command line option    *
* in place of the "-p" option.                              *
processing topology...
processing coordinates...

Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (dppc128.gro, 17365)
            does not match topology (dppc128.top, 0)

"One Cross Each" (Monty Python)

I don´t where the problem is, I've already checked the cpp compiler and
it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
topology file I have the following lines:

;    File 'dppc128.top' was generated
;    By user: onbekend (0)
;    On host: onbekend
;    At date: Tue Aug 18 10:02:52 2009
;    This is your topology file
;    Pure DPPC bilayer with 128 lipids and 3655 water molecules
; The force field files to be include
#include "ffoplsaa.itp"
; Include DPPC topology
#include "dppc.itp"
#include "lipid.itp"
#include "spc.itp"

[ molecules ]
; Compound   #mol
DPP          128
SOL          3655

If anyone can help It will be very nice,

Thank you very much so far,
Cíntia C. Vequi-Suplicy
Biophysics Group
Physics Institute
São Paulo University

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