Dear Justin, You are absolutely right. I only needed to keep the modified 'residuetypes.dat' in my working directory not the .rtp and .hdb files. I retried the whole process and this time CYA was not a separate group. Great experience. Thanks for your patience and help. Best,
Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 8:05 PM, Payman Pirzadeh wrote: > Since gromacs is globally installed on the cluster, I am making local > modifications. What was strange was I modified the three files, and I > ran pdb2gmx with them, and it failed (it could not find certain > atoms?!). Then I copied the whole gromos53a5 folder to my working > directory and moved these files into it, and I used the -ff option, > but it still opened the global folder. So, I kept the three modified > files in my working directory + the grooms folder with the modified > files, then it worked. The topology contained the new parameters. I > guess there might be sth with how pdb2gmx finds the database files. > The proper approach for making local modifications is to create a complete force field directory with all necessary files within it. The residuetypes.dat file must be in the working directory, not any subdirectory thereof, and you must issue all commands from within that directory. Otherwise, Gromacs programs revert to the copy in $GMXLIB. I suspect any of these factors will explain what you're observing with respect to intermittent successes - you're either moving around directories or putting files in the wrong place(s). -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
