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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