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As I said before, the demo is very outdated.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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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
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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 <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
========================================
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