Ms. Aswathy S wrote:
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.
Antechamber charges are not likely to be the proper way to replace PRODRG
charges for a GROMOS96 force field. Refer to the primary literature.
What time step did you use to get 2600 steps = 10 ps? Did the run actually
finish? Using a 4 fs time step would require 2500 steps, and a 2 fs step would
require 5000 steps. 2600 steps indicates a time step of 0.3846 fs. Somethings
seems wrong to me.
-Justin
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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--
========================================
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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