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? Sorry for inconveniences. 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 3:55 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 1:37 AM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for your suggestions. It all made sense. > But I ran into a strange problem. I checked the mail list, and all I > found was about misspelling the force field name. I copied the whole > gromos53a5.ff directory into my working folder, copied the modified > .rtp, .dat and .hdb files into the gromos53a5.ff folder, and issued: > pdb2gmx_d_mpi -f protein.pdb -p protein-CYA.top -o protein-CYA.gro > -inter -ff gromos53a5.ff but what I got was: > > Program pdb2gmx_d_mpi, VERSION 4.5.4 > Source code file: pdb2top.c, line: 239 > > Fatal error: > Could not find force field 'gromos53a5.ff' in current directory, > install tree or GMXDATA path. > For more information and tips for troubleshooting, please check the > GROMACS website at http://www.gromacs.org/Documentation/Errors > > If I do not add the -ff option, the default pdb2gmx command works, by > opening the force field from the default path. I tried 'source GMXRC' > from my working folder, but same error pops up. I am not sure what I > am missing here?! You're using the wrong syntax. The option -ff should take just the prefix of the force field directory, i.e. "-ff gromos53a5" which causes pdb2gmx to search for a gromos53a5.ff directory. -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
