Yes. I am doing that now. Thank you ery much.
Sent from Samsung Mobile <div>-------- Original message --------</div><div>From: Justin Lemkul <jalem...@vt.edu> </div><div>Date:02/09/2016 8:01 PM (GMT+05:30) </div><div>To: gmx-us...@gromacs.org </div><div>Cc: </div><div>Subject: Re: [gmx-users] Free energy calculation, Methane in water tutorial </div><div> </div> On 9/2/16 9:53 AM, sun.iba2 wrote: > Yes. But nothing else is printed on screen. Log files are creared but > incomplete. When I used perl script to generate respective .mdp files for > mininization and equilibrium, i found all of the generated files for 21 > lambda values were empty. However when I tried with my molecule, the 21 .mdp > files are created properly but still encountered same error with my file i.e. > .tpr file is missing. > This suggests something at the very top level is not set up correctly (paths, environment variables, etc). Run the commands in the job script interactively to figure out which step is failing. -Justin > > > > > <div>-------- Original message --------</div><div>From: Justin Lemkul > <jalem...@vt.edu> </div><div>Date:02/09/2016 4:57 PM (GMT+05:30) > </div><div>To: gmx-us...@gromacs.org </div><div>Cc: </div><div>Subject: Re: > [gmx-users] Free energy calculation, Methane in water tutorial </div><div> > </div> > > On 9/2/16 7:09 AM, Sun Iba wrote: >> Hello dear users >> >> I am following Justin's tutorial for free energy calculation of Methane in >> water. I have downloaded the job.sh file and trying to run it in terminal >> using: sh job.sh but it is giving following error: >> >> Program mdrun, VERSION 5.0 >> Source code file: >> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513 >> >> Can not open file: >> min0.tpr >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> >> Please help me with error. >> > > grompp failed to produce the .tpr file. Use the screen output to figure out > why. > > -Justin > -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
