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. '', 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- ======================================== 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 ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
