I was pretty confident that I am modifying the right file. apparently I did not access to the main file; so I asked my supervisor and he provided me with a proper access to the files.
Thanks again Justin. ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Monday, September 30, 2013 1:45:41 PM Subject: Re: [gmx-users] ionomer topolgy On 9/30/13 4:40 PM, Ehsan Sadeghi wrote: > Many thanks Justin. > > Apparently I was modifying the .rtp file in the wrong location; now the > pdb2gmx works and I can start the modelling. > In the future, make sure you're providing accurate answers to the questions being asked. I asked about this at least two or three times and was always assured that the modifications were being done properly. If you want free help, you have to make it easy! > I also have some concern about my pdb file. i generated from my drawing in > Avogadro, with some arbitrary bond length and angle. I hope that I can find > the correct bond length and angle with energy minimization; am, I right? > If done in vacuo, probably. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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
