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. 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 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:58 PM, Payman Pirzadeh wrote: > Hi, > Found my solution; made an index file which had the protein and CYA in > the same group. > Thanks for all your helps Justin. > I'm glad you found a solution, but for the purpose of being thorough I need to say that this should not be necessary. A residue listed as "Protein" in residuetypes.dat, if added prior to running pdb2gmx, should lead to seamless integration in the topology when running all subsequent steps in preparing the system. It is unclear to me what's going on here. -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
