Please try to hepl me.. Box[ 2]={ nan, nan, nan}
Can not fix pbc. Warning: Only triclinic boxes with the first vector
parallel to the x-axis and the second vector in the xy-plane are
supported. Box (3x3): Box[ 0]={ nan, nan,
nan} Box[ 1]={ nan, nan, nan} Box[ 2]={
nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the
first vector parallel to the x-axis and the second vector in the
xy-plane are supported. Box (3x3): Box[ 0]={ nan,
nan, nan} Box[ 1]={ nan, nan, nan} Box[
2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic
boxes with the first vector parallel to the x-axis and the second
vector in the xy-plane are supported. Box (3x3): Box[ 0]={
nan, nan, nan} Box[ 1]={ nan, nan,
nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. Warning: Only
triclinic boxes with the first vector parallel to the x-axis and the
second vector in the xy-plane are supported. Box (3x3): Box[ 0]={
nan, nan, nan} Box[ 1]={ nan, nan,
nan} Box[ 2]={ nan, nan, nan} Can not fix pbc.
------------------------------------------------------- Program mdrun,
VERSION 4.0.4 Source code file: nsgrid.c, line: 348
Fatal error: Number of grid cells is zero. Probably the system and box
collapsed.
-------------------------------------------------------
"Would You Like to Be the Monster Tonight ?" (Captain Beefheart)
OIn some pev Dept. Biotechnology Ext. 3108
----- Original Message ----- From: "Ms. Aswathy S"
<aswat...@amritapuri.amrita.edu> To: "Discussion list for GROMACS
users" <gmx-users@gromacs.org> Sent: Tuesday, June 16, 2009 12:40:04 PM
GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users]
problem in ngmx
hi justin,
your suggestions were helpful. Actually charges in the ligand topology
was having the problem. So I have added the charges from the
antechamber. Did Energy minimization. Now did an NVT equilibration of
10 ps. It finished at 2600 steps. But shows reasonable Energy and
Temperature (checked in the xmgrace). Seems it works fine..Now started
the NPT equilibration.
Thank you very much for your support.
Aswathy Dept. Biotechnology Ext. 3108
----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent:
Monday, June 15, 2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi Subject: Re: [gmx-users] problem in ngmx
Ms. Aswathy S wrote:
Hi Justin,
Thanks for the reply.
Once again i tried to minimize the protein +ligand in vacuum. Also
tried by varying the maximum force constant. But that too converged
at the 15 th step (or lesser steps based on the Fmax). The em.mdp
file i have attached here with. Please go through that once please
and tell me because of any of these parameters, the system behaves
odd??.
As I said before, it is not the step that matters, it is whether or not
the system converges within your criteria. I am assuming EM is
working, based on the fact that the process converges differently
depending on different target values for Fmax. Your .mdp file looks
reasonable.
If we can clarify for a moment - several messages ago you claimed that
you were doing a 20-ps NVT equilibration that was finishing at 15
steps, but that appears to not be the case. Is it the NVT step that is
failing to complete? Is ngmx failing to display the NVT trajectory, and
did gmxcheck report problems with the .edr file?
I think you are correct that the itp file created by PRODRG need
corrections. But how can I chek that is that the problem with that
file or how can i rectify?
Parameterization is very difficult. Prepare for a lot of advanced
work. Please see here:
http://oldwiki.gromacs.org/index.php/Parameterization
-Justin
Dept. Biotechnology Ext. 3108
----- Original Message ----- From: "Justin A. Lemkul"
<jalem...@vt.edu> To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org> Sent: Sunday, June 14, 2009 10:51:30 PM GMT
+05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users]
problem in ngmx
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"
<jalem...@vt.edu> To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org> 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"
<manik.ma...@gmail.com> To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org>, jalem...@vt.edu 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 <
domm...@icp.uni-stuttgart.de > wrote:
* Justin A. Lemkul < jalem...@vt.edu > [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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