[gmx-users] problem in gromacs 4?

[Justin A. Lemkul]

Several users have reported this problem, i.e.:

http://www.gromacs.org/pipermail/gmx-users/2008-November/038181.html

Perhaps try upgrading to version 4.0.2 and try again.

-Justin

Bernhard Knapp wrote:
> 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
> Bernhard
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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