Robert Selwyne wrote:
Dear GMX users
When i tried to rum grompp i get these errors. Would any one be able to
sort out this problem?
Sincerely
Robert
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grompp -v -f adp.mdp -po adpmdout.mdp -c genbox.gro -p genbox.top -o
gromppout.tpr
It would be easier to answer your question if you'd told us what you did
to generate genbox.gro and genbox.top. As it is, I'm going to have to guess.
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)
I guess that you've added solvent, and not updated the [molecules]
section of the .top file. Check chapter 5 of the manual if you don't
know how to do this or what I mean :-)
Mark
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