[gmx-users] Grompp error

[Justin A. Lemkul]

Cíntia C. Vequi-Suplicy wrote:
> Hello,
> 
> 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:
> 

Have you tried the advice from grompp to use -pp instead of -p?

General advice for this problem can be found here:

http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

Also an option is to upgrade to the most recent version of Gromacs (4.0.5), 
which does not require cpp.

-Justin

> ;
> ;    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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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