[gmx-users] error while running grompp

Ragothaman Yennamalli ymr79in at yahoo.co.in
Fri Jan 18 11:24:51 CET 2008

Dear all,
We are trying running Gromacs in different systems
with different number of processors. In sun opteron
cluster we checked and it ran perectly fine. When,
using the same input files, to run in apple g5 system
with same number of processors. I get the following
message when I run grompp:
 creating statusfile for 4 nodes...

Back Off! I just backed up mdout.mdp to
checking input for internal consistency...
calling /lib/cpp...
sh: line 1: /lib/cpp: No such file or directory
cpp exit code: 32512
Tried to execute: '/lib/cpp 
-I/Users/swadha/new_gromacs/share/top  master.top >
The '/lib/cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file
(confout.gro, 78268)
             does not match topology (master.top, 0)

I made new toplogy files, there is nil difference
between the new and old .top file used in grompp.
Still I get the same error message.

Please let me know where I am going wrong.



Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586

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