[gmx-users] problem running the demo

[Justin A. Lemkul]

Mao Mao wrote:
> Hi All,
> I ran into a problem when running the methanol example in "Getting 
> Started". When I ran "grompp -v", I got the following:
>   
>   Fatal error:
>   Atomtype CMET not found
> 
> I installed Gromacs 4.5.3 on Ubuntu and planned to learn the software. 
> Now I am stuck. 
> Many thanks for your help! I really appreciate it.
> 

There is a typo in the methanol.itp file in the /tutor/methanol subdirectory. 
Replace it with the one from the gromos43a1.ff directory.  There may be more 
errors along the way; I don't think the demo has been updated in some time.

-Justin

> Mao
> 
> 
> On Wed, Jan 5, 2011 at 4:41 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Mao Mao wrote:
> 
>         Hi All,
>         I am a new user of Gromacs and Linux. I am using Ubuntu 10.10
>         and installed Gromacs 4.5.3 following the instructions. When I
>         ran the demo, I found that when I pressed <enter>, the xterm
>         window which is supposed to appear separately just flashed and
>         disappeared immediately. For instance, "the output of the genbox
>         program should appear in a separate xterm window", but when I
>         pressed <enter> the window flashed and disappeared immediately.
>         Is there anything wrong that I need to fix or is that the way it
>         should be?
> 
> 
>     It is possible that something is wrong with the demo, but more
>     likely something is wrong with your X window settings.  If you're
>     looking for tutorial material, there are far better resources than
>     this simple walkthrough:
> 
>     http://www.gromacs.org/Documentation/Tutorials
> 
>     -Justin
> 
>         Best,
>         Mao
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================