[gmx-users] problem running the demo

[Mao Mao]

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?
Thank you very much.

Mao

On Tue, Jan 11, 2011 at 9:43 AM, Justin A. Lemkul <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>> 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
>>
>>    ========================================
>>    --     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
>
> ========================================
> --
> gmx-users mailing list    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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110117/52bf8c40/attachment.html>