Hi, Found my solution; made an index file which had the protein and CYA in the same group. Thanks for all your helps Justin.
P. -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 4:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:09 PM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for the tips. Things worked smoothly up to the point when I > wanted to run an actual simulation. When I wanted to run grompp for a > NVT simulation, I got this error message: > > Fatal error: > 7 atoms are not part of any of the T-Coupling groups > > I realized that that in my mdp file, I had: > > Tcoupl = Nose-Hoover > tau_t = 0.2 0.2 0.2 > tc-grps = Protein SOL CL- > ref_t = 310 310 310 > > I noticed that this warning is related to the CYA residue. So I added > CYA as a new group to the above list and problem was solved. But what > remains strange/scary to me is that I defined CYA in residuetypes.dat! > Shouldn't grompp consider the new residue as part of the protein? > Won't this separate temperature coupling of a residue and protein cause strange behavior? Yes, as does the fact that you're coupling ions separately from the solvent. If you correctly added CYA to residuetypes.dat, this shouldn't happen. Do not couple it separately from the protein; that makes no sense. -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
