[gmx-users] problem in gromacs 4?

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Mon Nov 24 16:24:29 CET 2008

Dear users

I am trying to minimize the energy of a complex using gromacs 4. The 
commands are the following:

pdb2gmx -f full_mCARKL_to_xylose_kinaseFH.pdb -o 
full_mCARKL_to_xylose_kinaseFH.gro.pdb -p 
full_mCARKL_to_xylose_kinaseFH.top -ignh
editconf -f full_mCARKL_to_xylose_kinaseFH.gro.pdb -o 
full_mCARKL_to_xylose_kinaseFH.cube.pdb -bt cubic -d 2.0
genbox -cp full_mCARKL_to_xylose_kinaseFH.cube.pdb -cs spc216.gro -o 
full_mCARKL_to_xylose_kinaseFH.water.pdb -p 
full_mCARKL_to_xylose_kinaseFH.top -nice 0

after genbox it stops with the error

Program genbox, VERSION 4.0
Source code file: gmx_genbox.c, line: 744

Fatal error:
Undefined solute box.
Create one with editconf or give explicit -box command line option

Although this is definitly not true since the box has been created with 
editconf (and not error is given by it). If I try the same commands (and 
complex) on Gromacs 3.3 it works fine without error. Any ideas?

Thank you in advance

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