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.
Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 5:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 7:25 PM, Payman Pirzadeh wrote: > I had modified three files: aminoacids.rtp, aminoacids.hdb and > residuetypes.dat. All these modifications were done prior running pdb2gmx. > So, I will be glad if you could let me know what the problem is. From that description, everything should be fine. Are you making local modifications (i.e. in the working directory with a copy of the force field) or making modifications in $GMXLIB? -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
