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)
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 -- 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
