Thanks for spotting that! I'd thought the system was complete when I'd done the index file - had completely forgot that I'd then gone onto generating ions!
Natalie xxx ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 10 December 2010 13:52 To: Gromacs Users' List Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile Natalie Stephenson wrote: > Hi, > > There are 101987 atoms in my system (2206 from my protein and the rest from > solvent and ions). The index file was made with make_ndx > after creating the solvated box > Command used was "make_ndx -f solv.gro" (solv.gro being the output from > genbox) > But then you added ions? You should make your .ndx file only after the system is complete, otherwise, if you've replaced a water molecule with an ion, the atom index for that atom will belong to a different group. -Justin > Natalie > xxx > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: 10 December 2010 12:26 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile > > Natalie Stephenson wrote: >> Hi, >> >> I've come across this error when performing grompp of my pull files >> before an afm simulation. I'm not really sure I understand why it's >> saying it ... I've checked over my index file and the atom is part of >> the solvent I've solvated the box with during genbox commands. >> >> The input on the grompp I performed was ... >> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.trr -o >> pull.tpr >> which produced the error below ... >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.5.3 >> Source code file: readir.c, line: 1371 >> >> Fatal error: >> Invalid atom number 101717 in indexfile >> ------------------------------------------------------- >> What is it I'm doing wrong?! :-S I'm not even really sure where the >> error lies with this one? Is it a step I've performed earlier that's >> incorrect? Can I just remove this atom from the index file and hope for >> the best? >> > > Never make ad hoc changes to any file that Gromacs produces unless you know > the > consequences of doing so. If make_ndx wrote that atom number, it did so for a > reason. > > How many atoms are in your system? How did you create the .ndx file? > > -Justin > >> Thanks loads >> Natalie >> >> >> mdp file I used is below ... >> >> title = Umbrella pulling simulation >> define = -DPOSRES_B >> ; Run parameters >> integrator = md >> dt = 0.001 >> tinit = 0 >> nsteps = 5000000 ; 10 ns >> nstcomm = 1 >> ; Output parameters >> nstxout = 50000 ; every 100 ps >> nstvout = 50000 >> nstfout = 5000 >> nstxtcout = 5000 ; every 10 ps >> nstenergy = 5000 >> ; Bond parameters >> constraint_algorithm = lincs >> constraints = all-bonds >> continuation = yes ; continuing from NPT >> ; Single-range cutoff scheme >> nstlist = 5 >> ns_type = grid >> rlist = 1.4 >> rcoulomb = 1.4 >> rvdw = 1.4 >> ; PME electrostatics parameters >> coulombtype = PME >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = Nose-Hoover >> nsttcouple = -1 >> tc_grps = Protein Non-Protein >> tau_t = 0.1 0.1 >> ref_t = 310 310 >> ; Pressure coupling is on >> Pcoupl = Parrinello-Rahman >> pcoupltype = isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocities is off >> gen_vel = no >> gen_temp = 310 >> gen_seed = 1 >> ; Periodic boundary conditions are on in all directions >> pbc = xyz >> ; Long-range dispersion correction >> DispCorr = EnerPres >> ; Pull code >> pull = umbrella >> pull_geometry = distance ; can't get PMF with direction >> pull_dim = N N Y >> pull_start = yes >> pull_ngroups = 1 >> pull_group0 = C-Terminal >> pull_group1 = N-Terminal >> pull_init1 = 0 >> pull_rate1 = 0.005 >> pull_k1 = 1500 ; kJ mol^-1 nm^-2 >> pull_nstxout = 1000 ; every 2 ps >> pull_nstfout = 1000 ; every 2 ps >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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? 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