Ms. Aswathy S wrote:
Hi Justin,
I tried maximum to find out the problem but i failed in that.
I will give you the detailed steps..Kindly check once and tell me where is the
problem. As you suggested now i am trying in gromacs 4.0.4 .
1. The ligand topology file is generated in PRODRG beta server using the GROMOS
96.1 force field.
2. The protein toplogy file using gromos 96 43 a1 force field
3. Tried to minimize in vacuum (Please find the em.mdp file). But the cycle
finished at 15 steps.
But in some previous post I saw that its not an error so I went ahead with
genbox and further minimization. But ended in the same 15 th steps.
also checked the gmxcheck for the files as you suggested it show the following
error.
What is most important is not the number of steps necessarily, but that the
potential energy converged to an appropriate value and you reached an Fmax below
your target.
Realize that using a topology straight from PRODRG is often not the best course.
The charges and charge groups assigned by PRODRG often require manual
modification and verification of the parameters. This could be a source of problem.
It may be that there is some kind of bug, but before that can be proposed, you
have to demonstrate that the preparation steps were successful (i.e., EM
criteria of potential energy and Fmax).
-Justin
'', 33685 atoms
Last frame 0 time 1.000
Both files read correctly
Checking energy file 1RBP_water_min.edr
-------------------------------------------------------
Program gmxcheck, VERSION 4.0.4
Source code file: enxio.c, line: 283
Fatal error:
Energy file 1RBP_water_min.edr not recognized, maybe different CPU?
-------------------------------------------------------
"I Do It All the Time" (Magnapop)
Am I doing any mistake in the steps???? Please find some time to help me.
Thank you very much,
Aswathy
Dept. Biotechnology
Ext. 3108
----- Original Message -----
From: "Justin A. Lemkul" <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
Sent: Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Re: [gmx-users] problem in ngmx
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) - (-7.40000e-03 6.79720e+00
6.07530e+00)
x[31428] ( 2.35365e-01 -6.53947e-03 5.65519e+00) - ( 2.35400e-01 -6.50000e-03
5.65520e+00)
x[31478] ( 1.54478e-02 6.14019e+00 5.74537e+00) - ( 1.54000e-02 6.14020e+00
5.74540e+00)
Segmentation fault
The energy minimisation & the equilibration steps are finished at 15 step
eventhough it was given for 20 ps(10000 steps).But the output coordinates file
doesnt show any abnornmality as i checked in the viewer? My equilibration step was
in NVT.
whether nothing is happening or any other problem?
If you got 15 steps when you expected 10000, it seems pretty clear to me that
something crashed very early on in your simulation.
-Justin
Thanks & regards,
Aswathy
Dept. Biotechnology
Ext. 3108
----- Original Message -----
From: "Manik Mayur" <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>, [email protected]
Sent: Saturday, June 13, 2009 5:34:08 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Re: [gmx-users] problem in ngmx
On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert < [email protected] > wrote:
* Justin A. Lemkul < [email protected] > [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 server
Xlib: No protocol specified
Can't connect to X Server.
Check your DISPLAY environment variable
Seems like your X environment is somehow not properly configured.
If you are working through ssh, then you can :
$export DISPLAY=<your current computer's ip>:0.0
Or you are tunneling through a SSH connection. There are several
possiblities:
1. Try ssh -X to login, this could solve the problem, if you are in
principle allowed to use X11 tunneling.
2. In case this does not work either it can be that you are not allowed
to tunnel X11.
However take care that you also need a properly configured XServer
running on your own system not just on the host you login. So in case
you use Windows or MacOS make sure this is the case.
Flo
************************************************
also the g_energy command shows that ,
Program g_energy_mpi, VERSION 3.3.3
Source code file: enxio.c, line: 239
Fatal error:
Energy file eq_2ps_ener.edr not recognized, maybe different CPU?
What does gmxcheck tell you about the file. Perhaps it has been corrupted in some way.
Also, you may want to work with a more current version (4.0.5) to utilize the newest features and bug fixes.
-Justin
Can any one help me, please???
Thanks,
Aswathy
ASBT
Dept. Biotechnology
Ext. 3108
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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