[gmx-users] Re: Genbox center of box

[Justin Lemkul]

On 6/10/13 2:33 PM, Matt Bawn wrote:
>> Can you please provide your exact sequence of commands (up to, and
> including,
>> genbox) and the exact error message (copied and pasted from the terminal)?
>> Which version of Gromacs are you using?
>
>
> I'm using Gromacs 4.5.5
>
> 1  pdb2gmx -f 2CCA_dw.pdb -o 2CCA_processed.gro -water spce -merge all
>
> FF 9
>
> 2  editconf -f 2CCA_processed.gro -o 2CCA_newbox.gro -c -d 1.0 -bt
> dodecahedron
>
>
>
> 3 $ genbox -cp 2CCA_newbox.gro -cs spc216.gro -o 2CCA_solv.gro -p topol.top
>
> GROMACS >  Enter coordinates of centre of box
>

I have never seen such a prompt, and I cannot reproduce the problem with version 
4.5.5 on my machine.  Did you install from source, or from some external binary 
or package manager?  Are you running Gromacs directly, or are you using any GUI 
interface of any sort?  Does the problem persist with a non-outdated version 
like 4.6.2?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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