[gmx-users] (no subject)

SLN Prasad Reddy sreeyapu at rediffmail.com
Wed Nov 24 16:53:46 CET 2004


Dear Gromacs users,
         I installed gromacs 3.1 and working on a protein having 247 amino acids ,ATP and Mg++. I could generate waterbox by using genbox command. When i tried "grompp" command to get "xxx.tpr" to use with "genion" command,it is showing following error. 

calling /lib/cpp...
sh: /lib/cpp: No such file or directory
cpp exit code: 32512
Tried to execute: '/lib/cpp  -I/usr/local/share/gromacs/top -DFLEX_SPC nbd.top > gromppAXEl1v'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file (box.pdb, 24489)
             does not match topology (nbd.top, 0)

I checked the number of coordinates in "box.pdb" and "nbd.top" and they are verymuch same.

 "grompp" seems to be not processing nbd.top. 

Kindly suggest me a solution. your suggestion will help me greatly.

Many thanks in advance


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