[gmx-users] problem in gromacs 4?

[Berk Hess]

Hi,

Indeed this bug has been fixed in 4.0.2.

Berk

> Date: Mon, 24 Nov 2008 11:00:46 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem in gromacs 4?
> 
> 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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