Hello all. Just a quick clarification, please.
Reading the original GROMOS53A6 paper, it appears that 2nd neighbor (1-3)
interactions are always excluded, and that third neighbor (1-4) non-bonding
interactions are used, yet modified in some circumstances. The paper also
states that all (1-4) inter
Ms. Aswathy S wrote:
Thank you very much for the reply...
gmxcheck of my out shows a "segementation fault" in the last part. What could
be the problem??
this is the last part of the output
x[31416] (-7.37978e-03 6.79718e+00 6.07531e+00) - (-7.4e-03 6.79720e+00
6.07530e+00)
x[31428
Thank you very much for the reply...
gmxcheck of my out shows a "segementation fault" in the last part. What could
be the problem??
this is the last part of the output
x[31416] (-7.37978e-03 6.79718e+00 6.07531e+00) - (-7.4e-03 6.79720e+00
6.07530e+00)
x[31428] ( 2.35365e-01 -6.53947e
On Sat, 2009-06-13 at 17:34 +0530, Manik Mayur wrote:
> Seems like your X environment is somehow not properly
> configured.
>
> If you are working through ssh, then you can :
>
> $export DISPLAY=:0.0
Ugh, that's the archaic, telnet epoch way of doing it. It doesn
On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert <
domm...@icp.uni-stuttgart.de> wrote:
> * Justin A. Lemkul [2009-06-13 07:31:17 -0400]:
>
>
>>
>> Ms. Aswathy S wrote:
>>
>>> Hi,
>>>
>>> after equlibration of my protein and ligand I tried to create the energy
>>> file ans well as the to display
* Justin A. Lemkul [2009-06-13 07:31:17 -0400]:
Ms. Aswathy S wrote:
Hi,
after equlibration of my protein and ligand I tried to create the energy file
ans well as the to display the trajectories using ngmx option,. But it shows
the follo: error,
Xlib: connection to ":0.0" refused by serv
abelius wrote:
Since the charges / bond lengths and angles were obtained for QM
calculations for the excited state of TRP I'm wondering if it would make
sense to apply the alternative bond lengths and keep the force constants
of TRP in the ground state?
I guess it's really going to depend o
If you're asking a new question, please start a new thread; it helps keep the
archive clean of unrelated search results.
Omer Markovitch wrote:
How many letters for residue name are allowed in the PDB format? Omer.
The first Google result for "PDB format" points to:
http://www.wwpdb.org/
Ms. Aswathy S wrote:
Hi,
after equlibration of my protein and ligand I tried to create the energy file
ans well as the to display the trajectories using ngmx option,. But it shows
the follo: error,
Xlib: connection to ":0.0" refused by server
Xlib: No protocol specified
Can't connect to X
Hi,
after equlibration of my protein and ligand I tried to create the energy file
ans well as the to display the trajectories using ngmx option,. But it shows
the follo: error,
Xlib: connection to ":0.0" refused by server
Xlib: No protocol specified
Can't connect to X Server.
Check your DISPLA
How many letters for residue name are allowed in the PDB format? Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
___
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http://lists.gromacs.org/
Please ignore this post. I rectified the problem by using the GMXLIB export.
Thank you very much for all the support
Aswathy
Dept. Biotechnology
Ext. 3108
- Original Message -
From: "Ms. Aswathy S"
To: "gmx-users"
Sent: Saturday, June 13, 2009 12:00:11 PM GMT +05:30 Chennai, Kolkata,
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