[gmx-users] problem running the demo

[Justin A. Lemkul]

Mao Mao wrote:
> Hi Justin,
> I tried the "mixed" example today and when I ran grompp -v I got the 
> following error:
> 
> Fatal error:
> Topology include file "methanol.itp" not found
> 
> Could you help me with that?

As I said before, the demo is very outdated.  I will file a redmine issue so 
this gets updated eventually.

There is no "methanol.itp" file in the "mixed" directory.  Either copy the one 
from the "methanol" example there, or supply an appropriate "include" path in 
grompp.mdp.

You would probably learn quite a bit more about Gromacs (including how to deal 
with common errors like this one) from doing some real tutorials:

http://www.gromacs.org/Documentation/Tutorials#General

-Justin

> Thank you very much.
> 
> Mao
> 
> On Tue, Jan 11, 2011 at 9:43 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>            ========================================
>            --     gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>            <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 
>            http://lists.gromacs.org/mailman/listinfo/gmx-users
>            Please search the archive at
>            http://www.gromacs.org/Support/Mailing_Lists/Search before
>         posting!
>            Please don't post (un)subscribe requests to the list. Use the www
>            interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>
>            <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
> 
>            Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

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

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

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