[gmx-users] Fatal Error in grompp

cseager at ucla.edu cseager at ucla.edu
Thu Dec 15 09:29:29 CET 2005


I would appreciate some help with this small problem.  I have searched 
the archives and found similar problems, but none of the solutions seem 
to fit my particular situation.

When running grompp, I get the fatal error:

checking input for internal consistency...
...ling /usr/bin/cpp
: No such file or directory
cpp exit code: 32512
dwb.top > grompp1UTIs9'are/gromacs/top ' command is defined in the .mdp file
processing topology...
processing coordinates...
Program grompp, VERSION 3.3
Source code file: grompp.c, line: 427

Fatal error:
number of coordinates in coordinate file (dwb.gro, 81)
             does not match topology (dwb.top, 0)

I have recognized the possibility of a problem with the location of cpp 
in my .mdp file, however I have checked the location of my cpp and 
found it to be in /usr/bin/cpp, so that cannot be the problem.  Also, I 
read through the manual and so far can't see any problems with the form 
of my .top file.  The particular files I am using work well on another 
computer set up to use GROMACS version 3.2, whereas on my computer I am 
using version 3.3.  I am operating on a Mac OS X 10.4.  Since the 
manual is version 3.2, I am wondering if this is the problem, though I 
compared my .top file to some .top files in the gromacs demo files and 
could not see any significant differences.  Any suggestions would be 

Much Appreciated

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