[gmx-users] topology doesnt match

Triguero, Luciano O ltriguero at miami.edu
Mon Apr 2 17:14:10 CEST 2007

Check if you have all group types in your mdp file.
Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938


From: gmx-users-bounces at gromacs.org on behalf of Robert Selwyne
Sent: Mon 4/2/2007 10:40 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] topology doesnt match

Dear GMX users
When i tried to rum grompp i get these errors. Would any one be able to
sort out this problem?
grompp -v -f adp.mdp -po adpmdout.mdp -c genbox.gro -p genbox.top -o

creating statusfile for 1 node...

Back Off! I just backed up adpmdout.mdp to ./#adpmdout.mdp.1#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
WARNING 1 [file "genbox.top", line 283]:
  System has non-zero total charge: -3.000000e+00

processing coordinates...
Fatal error: number of coordinates in coordinate file (genbox.gro, 3516)
             does not match topology (genbox.top, 33)

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